The below are openly linked with Scientology:
Applied Scholastics
Association for Better Living and Education (ABLE)
Author Services, Inc.
Bridge Publications, Inc.
Church of Spiritual Technology (COST)
Citizens Commission on Human Rights
Criminon
Dianetics
Drug-Free Marshals ( aimed at children)
Freedom Magazine
Golden Era Productions
Hubbard Colleges of Administration
International Association of Scientologists(IAS)
Narconon
Office of Special Affairs
Religious Technology Center
Scientology Missions International (SMI)
Scientology Volunteer Ministers
Way to Happiness Foundation
World Institute of Scientology Enterprises - WISE
Controlled by CoS but coy about it:
Business Success Sales and Management Training
Csas Dolce Casa
Child Guidance Centers
Citizens for an Alternative Tax System
Community Service Guild
Computer Ethics Institute(CEI)
Concerned Businessman's Association of America
Cry Out
Education Alive
Effective Management Centers (EMC)
Environmental Task Force
Foundation for the Advancement in Science and Education (FASE)
Health Med
Lead the Way to a Drug-Free USA
Library Donation Service
National Association for Rights Protection and Advocacy (NARPA)
Religious Freedom Crusade
Stop Torture of Mental Patients (STOMP)
These came from this list, which also discusses the organizations. I disagree with placing Earthlink on the list. It has thousands of non-Scientology employees who would be hurt by a boycott, and nothing has been proven that CoS influences Earthlink.
http://www.b-org.demon.nl/scn/infiltration/front-orgs.html