Ha, MST3K as #1, guess I should have seen that coming but I never think of it as science fiction at all, pure comedy for me....
Kind of shocked that the original BSG made it on but Space 1999 didn't. That's the only major oversight I can think of. Only ones I would quibble over being on the list are the Batmans and I guess 3rd Rock From The Sun.
Here's mine (forgot Futurama, not sure where I'd place it, maybe 9th, and kick Earth 2 off):
1 Battlestar Galactica 2004
2 Star Trek (TOS)
3 Doctor Who
4 Star Trek Next Generation
5 Stargate SG-1
6 Firefly
7 Babylon 5
8 Star Trek Deep Space 9
9 Stargate Atlantis
10 Enterprise
11 Red Dwarf
12 Space 1999
13 Farscape
14 Eureka
15 Torchwood
16 Warehouse 13
17 Star Trek Voyager
18 Blake's 7
19 Voyage To The Bottom Of The Sea
20 Andromeda
21 Battlestar Galactica 1978
22 SeaQuest DSV
23 Lexx
24 Earth 2
25 Lost In Space