This is only for television shows, not movies. And just science fiction (not fantasy).

So far, after some brainstorming with a couple of friends, I have come up with the following list, but looking for more (once nominations are done, I'll turn it into a series of QuickPolls):

Dana Scully/Fox Mulder (X-Files)
Olivia Dunham/Peter Bishop (Fringe)
Malcolm Reynolds/Inara Serra (Firefly)
Delenn/John Sheridan (Babylon 5)
Marcus Cole/Susan Ivanova (Babylon 5)
John Crichton/Aeryn Sun (Farscape)
Vala Maldoran/Daniel Jackson (Stargate SG1)
Jack O'Meill/Samantha Carter (Stargate SG1)
Rodney McKay/Jennifer Keller (Stargate Atlantis)
Matther Scott/Chloe Armstrong(Stargate Universe)
Ronald Greer/Lisa Park (Stargate Universe)
Everett Young/Tamara Johansen (Stargate Universe)
Kara Thrace/Lee Adama (RDM's BSG)
Bill Adama/Laura Roslin (RDM's BSG)
Gaius Baltar/Caprica Six (RDM's BSG)
Galen Tyrol/Callie Henderson (RDM's BSG)
Amy Pond/Rory "Pond" (Doctor Who)
The Doctor/River Song (Doctor Who)
Simon Bellamy/Alisha Baily (Misfits)
Jack Carter/Allison Blake (Eureka)
Jo Lupo/Zane Donovan (Eureka)
T'Pol/Charles "Trip" Tucker (Star Trek Enterprise)
William Ryker/ Deanna Troi (Star Trek Next Generation)
Tom Paris/B'Elanna Torres (Star Trek Voyager)
Al Calavicci/Beth Calavicci (Quantum Leap)

I admit, there are plenty of SF shows that are not represented (such as Lost, which I and my buddies Tony and Doug do not know well enough to know any of the romances).

Please add any other relationships we missed.

(Oh, and yes, some of those listed above were not fleshed out, such as Mal/Inarra and the Ivanova/Marcus* romance never had a chance to develop, but it was still basically there; as I stressed, this was just a brainstorming session that produced the list above)

*I'm pretty sure that if Claudia Christian hadn't left the show after season 4, Ivanova would have had a visit from Marcus in the season 5 episode "Day of the Dead" instead of Lochley's crappy visitation from her old drug buddy; that would have made this episode SO MUCH MORE potent emotionally I think.