It looks like the independent Thompson DNA project site
http://www.thompsonfamilies.org has been quasi-abandoned. They used ybase as their default database. I did get in touch with them long enough to enter my results, but then never heard back from them. I heard from a person on one of the DNA users groups that the administrators need help. Right now the person in charge is Kathy Borges (spelling?). She's also deeply involved in ISOGG and that takes most of her time. From other posts on the DNA Newbies user group she also seems to be heavily involved in the ideas and technology used in the family finder process (although it's pretty advanced stuff and fairly confusing to me).
Family Tree DNA seems to be the king of the family projects. As someone who tested with Ancestry.com I can say that it's critical to find out what your numbers would be at FTDNA and learn to speak about them in FTDNA's order if you want to be able to converse with others. The only company I see mentioned more on the DNA newbies group is 23 and me. FTDNA has a free database at ysearch.org, but I've heard some complaints that it's records don't get updated when people upgrade to newer tests (like when they move from 37 markers to 68 or whatever). The other drawback is that it is limited to YDNA.
Genetree, Genebase, SMGF, Ybase and Ysearch all allowed me to put in my numbers for free and search their databases. Maybe we could link to all these sites as possible search areas for members with any tips and tricks we've picked up to help in their search?
Genetree, SMGF and Ancestry.com happen to use Sorenson Genomics as their testing company. Ybase is set up by DNAHeritage, Genebase may be a DNAheritage company as well. Genetree and Genebase also feature MTDNA searches.
I think for right now, Family finder is in a class by itself because it looks at more than just Y and mitochondrial DNA and actually checks 22 chromosomes. I'm sure it will be the standard of the future though. I'm not sure what other companies offer autosomal testing.