Well, in going with my "strange" theme, what I like is almost certainly not going to be the most popular, even among sci-fi fans ;-)
I think the original Prisoner (not the recent tortuous remake) was one the best TV series of all time. However, many would not consider it sci-fi.
"Brazil" certainly is among my top movies of all time, but its dark humor is not for everyone. On the low-budget front, I am a fan of "Dark Star." Another top favorite is "Donnie Darko."
Do I have a dark theme going here?