A number of researchers, and of course Scientology’s PR people and shills, over many years have written about the relationship, and many of its relevant incidents and connections have already been established. Scientology's obsessive revisionism when it comes its founder's past will make it advisable for the foreseeable future to occasionally revisit and re-establish the facts.
Russell Miller's Bare-faced Messiah provides a basic backdrop for the Heinlein relationship:
In Bare-Faced Messiah,Russell Miller wrote:As an editor, [John W.] Campbell used his magazine to speculate on the implications - emotional, philosophical and sociological - of future scientific discoveries. He expected style, skill, ingenuity and technical proficiency from his contributors. Few of the existing pulp writers could meet his exacting standards and so he set out to nurture new talent. Almost all the biggest names of the Golden Age - Isaac Asimov, Robert Heinlein, A.E. van Vogt and many others - were first published in Astounding. (p. 77)
While he was at Princeton, Ron was invited to join a group of science-fiction writers who met every weekend at Robert Heinlein's apartment in Philadelphia to discuss possible ways of countering the Kamikaze menace in the Pacific. They were semi-official, brainstorming sessions that Heinlein had been asked to organize by the Navy, in the faint hope of coming up with a defence against young Japanese pilots on suicide missions. 'I had been ordered to round up science fiction writers for this crash project,' Heinlein recalled, 'the wildest brains I could find.'
Heinlein's apartment was only three hundred yards from Broad Street Station in downtown Philadelphia and the group gathered on Saturday afternoons, arriving on Pennsylvania Railroad trains which ran every half hour into Broad Street. 'On Saturday nights there would be two or three in my bed,' said Heinlein, 'a couple on the couch and the rest on the living-room floor. If there was still overflow, I sent them a block down the street to a friend with more floor space if not beds.'
Heinlein tried to avoid asking Ron to walk down the street as Ron had said that both his feet had been broken when his last ship was bombed. 'Ron had had a busy war - sunk four times and wounded again and again,' Heinlein explained sympathetically.
Sunday morning was set aside for the working session, after which everyone sat around swapping stories and jokes. Ron often got out his guitar and entertained them in a rich baritone voice with songs like 'Fifteen Men on a Dead Man's Chest' and 'I Learned about Women from Her'. He could also reduce the assembled company to helpless laughter with his repertoire of fast-moving burlesque skits in which he played all the roles.
15. Deck log of USS Algol, US National Archives
16. Foreword to Godbody by Theodore Sturgeon, 1986
On Saturday 2 December, Jack Williamson, then a Sergeant in the US Army, hosted a dinner in Philadelphia for fellow science-fiction writers and their wives. He was to be sent overseas in a couple of days and this was his farewell party. Among those present were the Heinleins, the de Camps, the Asimovs and L. Ron Hubbard. 'The star of the evening', Isaac Asimov recalled, 'was Ron Hubbard. Heinlein, de Camp and I were each prima donna-ish and each liked to hog the conversation - ordinarily. On this occasion, however, we all sat as quietly as pussycats and listened to Hubbard. He told tales with perfect aplomb and in complete paragraphs.'
The host was less impressed. 'Hubbard was just back from the Aleutians then,' said Williamson, 'hinting of desperate action aboard a Navy destroyer, adventures he couldn't say much about because of military security.
'I recall his eyes, the wary, light-blue eyes that I somehow associate with the gunmen of the old West, watching me sharply as he talked as if to see how much I believed. Not much.'
Heinlein's group never came up with any ideas about how to prevent US Navy losses from Kamikaze pilots, but it did not matter much because the war was drawing to a close and Japan was running out of aircraft and pilots to fly them. The last big Kamikaze strike was launched in January 1945 against the US fleet (including Ron's old ship, the USS Algol) taking part in the invasion of Luzon. That same month Ron was transferred to the Naval Civil Affairs Staging Area in Monterey, California, for further training, having finished about mid-way among the 300 students on his course at the school of Military Government. In April he again reported sick and a possible ulcer was diagnosed. (p. 109-110)
17. Asimov, op. cit.
18. Williamson, op. cit.
Miller, R. (1987). Bare-faced messiah: The true story of L. Ron Hubbard. (HTML Version 2 (22 Nov 1997).
Chris Owen's Ron the "War Hero" is an indispensable account of Hubbard's navy record and of his stolen valor. The issue of Hubbard's false medal claims has entered the criminality realm since the US passed the Stolen Valor Act, and has become immediately relevant in Scientology's dealings with The New Yorker.
In this excerpt, Owen appears to have borrowed liberally from Miller in his description of the early brainstorming sessions in Philadelphia.
In Ron the "War Hero", Chris Owen wrote:While [Hubbard] was at Princeton, he was invited to join a group of science-fiction writers who met every weekend at Robert Heinlein's apartment in Philadelphia to discuss possible ways of countering the Kamikaze menace in the Pacific. They were semi-official, brainstorming sessions that Heinlein had been asked to organize by the Navy, in the faint hope of coming up with a defence against young Japanese pilots on suicide missions. "I had been ordered to round up science fiction writers for this crash project," Heinlein later commented, "the wildest brains I could find." 
Heinlein recalled that he had tried to avoid asking Hubbard to walk down the street as the latter had said that both his feet had been broken when his last ship was bombed: "Ron had had a busy war - sunk four times and wounded again and again."
Another of the group, Jack Williamson, then a Sergeant in the US Army, held a dinner on December 2, 1944 for his fellow writers and their wives. Hubbard told his colleagues of his adventures earlier that year. "Hubbard was just back from the Aleutians then," said Williamson, "hinting of desperate action aboard a Navy destroyer, adventures he couldn't say much about because of military security ... I recall his eyes, the wary, light-blue eyes that I somehow associate with the gunmen of the old West, watching me sharply as he talked as if to see how much I believed. Not much." 
 Heinlein, foreword to Godbody, Theodore Sturgeon, 1986
 Williamson, Wonder's Child: My Life in Science Fiction, 1984
Owen, C. (1999). Ron the "War Hero": L. Ron Hubbard and the U. S. Navy. Retrieved 23 January 2011 from http://www-2.cs.cmu.edu/~dst/Cowen/warhero/crippled.htm
Jon Atack gives a quick nod to the sci fi angle in his 1990 exposé.
In A piece of blue sky: Scientology, Dianetics, and L. Ron Hubbard exposed, Jon Atack wrote:Hubbard joined editor John Campbell's circle of friends, and became a major contributor to the reshaping of science fiction which Campbell brought about. Campbell was also to figure in the birth of Dianetics, twelve years later. Recently this pre-war period has been dubbed the Golden Age of Science Fiction. Hubbard's work appeared alongside that of Robert Heinlien [sic], A.E. van Vogt, and Isaac Asimov, each of whom has stated his admiration for Hubbard's stories. Although Hubbard's writing was patchy in places, he certainly had a very inventive imagination. He became a regular contributor to Astounding, moving back to New York in the autumn of 1939.
Atack, J. (1990). A piece of blue sky: Scientology, Dianetics, and L. Ron Hubbard exposed. Retrieved 23 January 2011 from http://www.cs.cmu.edu/~dst/Library/Shelf/atack/bs2-3.htm
Corydon, in Messiah or Madman mentions that Heinlein was a "one-time friend of Hubbard's."
In L. Ron Hubbard: Messiah or Madman?,Bent Corydon wrote:When viewing the Commodore's ship Apollo, the law to be adhered to was more like, "Do What Ron Wilt," the officers and crew being subjected to the strictest of rigors, while Ron did as he pleased. His will was supreme.
Robert Heinlein, a one-time friend of' Hubbard's, suggested this well in a recent novel. He referred to his followers as "L. Ronners" and "Hubbardites." Some ex-Scientologists use the term "Rondroids." The stable dictum for his followers is his written or spoken intention: "Do WHAT RON SAYS."
Corydon, B. (1987). L. Ron Hubbard: Messiah or Madman? clambake.org. Retrieved on 23 January 2011 from http://www.clambake.org/archive/books/mom/Messiah_or_Madman.txt.
In the Snake Thompson thread, I posted a quote from William Sim Bainbridge's "The Cultural Context of Scientology". In the following excerpt from the same essay, published in Scientology (2009), Bainbridge mentions Heinlein as one of the authors in the Astounding circle, and gives him a special mention as the "dean" of science fiction.
In The Cultural Context of Scientology, William Sims Bainbridge wrote:Mr. Hubbard really had two careers as a science fiction writer. First, from about 1938 until the establishment of Dianetics in the early 1950s, he was one of a stable of authors associated with Astounding Science Fiction, edited by John W. Campbell, Jr., the flagship of the so-called golden age of science fiction (Rogers, 1964). His second career consisted of a series of epic novels, beginning in 1982 with Battlefield Earth, which was made into a movie in 2000 starring John Travolta, a Scientologist. Among the other authors in the Astounding circle who were close to Mr. Hubbard especially worth mentioning are the "dean" of science fiction writers, Robert A. Heinlein, and A. E. Van Vogt.
Lewis, J. R. (Ed.). (2009). Scientology. New York ; Oxford: Oxford University Press.
Bainbridge goes on to provide a detailed analysis of popularity polls on Hubbard, Heinlein, E.E. Doc Smith, Asimov, Chandler, Budrys, and Van Vogt, along with a graph to "show how the subculture of science fiction "fandom" has changed its views of some of the older writers."
Interestingly, in another article published in Scientology, Andreas Grűnschloβ links the Xenu incident to Heinlein's Stranger in a Strange Land.
In Scientology, a "New Age" Religion?, Andreas Grűnschloβ wrote:This UFOlogical connection is explicitly apparent in the foundation myth of Scientology's "Operating Thetan" (OT) anthropology. According to the secret doctrines of Scientology—which are nowadays far from arcane, as information about court trials and other disclosures by former members appear in hundreds of pages on the Internet—there once was a fierce intergalactic ruler named Xenu, who brought millions of thetans to this Earth (which back then carried the name Teegeack"), and that is how their (i.e., our) life started in this region of the universe ("sector nine"). Amazingly, this story, which forms the central core myth in OT level III initiation teachings,  was rewritten by Hubbard as a mere science fiction novel in the late 1970s. As such, it carries the title Revolt in the Stars, and it has so far not been officially published. Copies of the manuscript circulate every now and then on the Internet. It is an amazing piece and trustworthy in terms of Hubbard's authorship—according to style, phrasing, and content. This oscillation between the production of mythic core stories and mere fantasy tales is also a characteristic typical of modern esoteric traditions: Helena P. Blavatsky, for example, wrote fantasy tales beside her theosophical disclosures,  and Charles Hoy Fort's alternative, anomalistic science in his Book of the Damned (and the three follow-up volumes)  inspired fantasy authors like H. P. Lovecraft as well as esoteric seekers. Erich von Daniken, working along Charles Fort's lines, also oscillates between fantasy and fringe historiography/archaeology, and his "Ancient Astronaut" stories have often been often reabsorbed by esoteric and UFO-believing groups. The framework story in Hubbard's Revolt in the Stars does, by the way, include the idea of a time capsule in the vein of the Ancient Astronauts' scheme.[31 ]
 Robert Kaufman, Inside Scientology (London: Olympia Press, 1972) was among the first (if not the first) to publish a disclosure of this mythic story. Nowadays, even copies of Hubbard's handwritten sheets containing this story are circulating on the Internet.
 It contains Hubbard's typical imagery of women, an evil psychiatrist, on the other hand "loyal officers," and the usual Star Wars scenario inside a "Galactic Confederation." Compared to other published fictional writings by Hubbard, it appears very genuine. (Probably due to legal reasons, no existing copy could be located via Web searches at the moment.) The story contains the struggle between the intergalactic ruler Xenu and the "loyal officers" who, in the end, manage to overthrow his despotic rule after he murdered all disobedient subjects on the "extermination site" earth by bombing them on volcanoes (cf. esp. chapter 14).
[28.] Cf. Marco Frenschkowski, "Okkultismus und Phantastik: eine Studie zu ihrem verhaltnis am Beispiel der Helena Petrovna Blavatsky," in: Das Schwarze Geheimnis. Magazinfur unheimliche Literatur 4 (1999): 53-104. Or, take Heinlein's science fiction novel "Stranger in a Strange Land," which in turn inspired the formation of a neo-pagan movement calling itself actually "Church of all Worlds," like the neo-Martian religion in the novel. One could go on to the Star Trek culture, to Heaven's Gate, and the Raelians.
Lewis, J. R. (Ed.). (2009).Scientology. New York ; Oxford: Oxford University Press.
Adam Rostoker (1959-1997) argued that Robert A. Heinlein wrote Stranger in a Strange Land as an "allegorical recapitulation of Thelema" and linked Stranger to the Babalon Working through the words of Parsons' "scribe," L. Ron Hubbard.
In Whence Came the Stranger: Tracking the Metapattern of Stranger in a Strange Land, Adam Walks Between Worlds wrote:In 1961 Robert Anson Heinlein published a novel about a young Martian named Valentine Michael Smith. The book, Stranger in a Strange Land (Stranger), burst from its modest initial reception in science fiction circles to become one of the most influential works of the 20th century. Its concepts molded the critical thinking of many important social movements and paved the way for that astonishing period of social, religious, and sexual reclamation that is misleadingly dubbed "the 60s." Arriving, as it did, at a nadir of American free thought and at a peak of media censorship, Stranger's publication was a minor miracle and its later mainstream success has always been considered a first class fluke. It became the first science novel to penetrate public consciousness since the days of Verne and Wells and initiated an unprecedented era of respectability for science fiction that opened the door for the Star Trek, 2001 and Star Wars. Stranger also marked a radical departure of form, not only for the author, but for American thought and expression in general. Stranger was the quintessence that transformed the nation's repressively conformist, post-war paranoia into the overtly sensual, erudite, cynical optimism that epitomized the years preceding the Reagan administration.
This recalls Heinlein's link with Parsons. As a part of the Babalon Working, Parsons 'received' a short 'book' entitled Liber 49 or The Book of Babalon. Parsons claims it was the fourth chapter to Liber Legis, a claim which made him less than popular with Crowley and the OTO. Regardless of this claim, it is a powerful text that deals mostly with the coming of the Thelemic heir. There are two parts in particular that stand out after reading Stranger. The first is part of the channeled instructions to Parsons for the ritual -- it advises him to clear his mind in preparation: "Consult no book but thine own mind. Thou art god. Behave at this altar as one god before another."  It is interesting to note that these words were mouthed, not by Parsons, but by his Scribe, L. Ron Hubbard, who was close friends with Heinlein at about the same time the latter was working on his first shot at Stranger. The other Babalon Working quote which stands out, and there are many quotes which are not so overt, comes from Liber 49 which Parsons channeled alone out in the desert -- e.g., sans Hubbard: "37 For I am BABALON, and she my daughter, unique, and there shall be no other women like her. 38. In My Name shall she have all power, and all men and excellent things, and kings and captains and the secret ones at her command. 39. The first servants are chosen in secret, by my force in her - a captain, a lawyer, an agitator, a rebel - I shall provide." (Italics added)
 Most of "the 60s" as a popular movement didn't even start until around '65 and didn't really end until well after Nixon got re-elected in '72. The most active period occurred between 1968-74 and in fact, most of "the '60s" are still happening. Referring to "the 60s" quarantines a radical, ongoing, whole systems transition and reduces it to a mere historical fad.
 The Collected Works of Jack Parsons, OTO, NY from the "First Ritual of the Book of Babalon".
Adam Walks Between Worlds (Adam Rostoker) (1993). Whence Came the Stranger: Tracking the Metapattern of Stranger in a Strange Land. Retrieved on 18 January 2011 from http://firehead.org/~pturing/occult/grok/thelema.htm. Also at http://www.greylodge.org/occultreview/glor_002/stranger.htm
Edit: Added a link to the Snake Thompson thread.