I find it very interesting that you made this thread, because while I was out driving today, I was thinking about what my favorite doujin album is. For a few years now, I have collected all of it in a folder aptly titled "DOUJIN", which includes everything I've gathered from OCRemix, VGMix, Dwelling of Duels, S.S.H., random internet searches, as well as the actual CD releases.
Excluding all vgm doujin given away for free via downloads, my favorite is HIGHSPEED ∇ - Romancing SaGa Battle Guitar Arrange CD. Some doujin albums are uneven, unprofessional, or simply worse than the free stuff. If I have to pay for a doujin album, then I expect it to, at the very least, be superior to the free stuff. Highspeed is like a fusion of Guilty Gear and Dracula Battle. It's fast and even, which means the tracks sound relatively the same, unlike some other doujin albums, which vary from low quality to high quality. Everything is very high quality on Highspeed and it makes me want to investigate the Saga Frontier soundtrack a little more closely. I already know that Romancing Saga 1-3 are incredible, but I've somehow forgotten about Saga Frontier. This definitely destroys the Mega Man album the group has previously released; I've been listening to this repeatedly, with no sign of becoming bored.
My favorite of all the free albums is Super Metroid - Relics of the Chozo. My $2100 headphone system has found subtleties here that are very impressive. I can't believe this was free.
I have more than 600 individual fan-made songs, so it would be difficult to pick a favorite. I've downloaded more than 2,000, easily. Those 600+ are my favorites, so you can see the problem in choosing just one. If I were locked in a room and I had to pick one before being allowed to leave, I'd probably go with this one.