I was comtemplating voting for Blake Stone: Aliens of Gold. I had that game as a child and really liked it. But looking at it about 10 years later...it just seems to lack that "something". I don't know, certainly you don't have to agree. I'm in the process of playing Planet Strike and ROTT for the first time. ROTT seems to have the most potential. Never cared for C7 or OP:BC much. Other games (like Noah's Ark or that sort) I've never really thought about looking at, but I left the option in just in case one of you find one of those games to be the most fun of all.
Of course, the original Wolf3D is also great, it's a classic, and would be close second vote to SOD for me. Don't like the SOD mission packs as much though, esp. Return to Danger.
In addition to the main poll I'd also be interested in just (roughly) how you'd order them for fun value (at least the ones you have) - or even descriptions like I've posted above.