Too many to list but I'll try to narrow it down & only listing ones I love based on the whole soundtrack not just main theme.
(no particular order)
Serenity, one of the best sci-fi movies if not they best of the last two decades (the best ever in my opinion) & has a fantastic Soundtrack to boot. David Newman (Galaxy Quest, Anastasia, The Flintstones, War of the Roses) creates a wonderful main theme during the opening credits, & River's theme used a few times throughout the OST stand out not only cause its touching & beautiful but because Newman actually bought a Piano which was a little broken to play River's theme on adding so much to that theme (River=broken), composers like deserve an oscar.
Batman '89/Returns, easily the best Batman music ever produced (along with the 60's theme

), Danny Elfman at his truly best, & that THEME.
Wing Commander, may not be one of the greatest films (but certainly amoung video game movies) it has one of the best Military based themes ever created (goosebumbs everytime), composed by David Arnold (last 4 Bond films, Independence Day, Stargate), a hugely underrated soundtrack.
Thunderbirds (2004 film), bollocks film adaption of the classic puppet series but Hans Zimmer creates something hugely different here other than his usual Gladiator-Pirates of the Caribbean-BB-TDK remix.
Casino Royale, my favourite of all the Bond OST's, David Arnold truly shines here from Vesper's Theme to Miami Airport to The Name Is James Bond, all fantastic tracks, shame the song "You Know My Name" wasn't added to the Soundtrack.
Judge Dredd, I'm not listing OST's just for their Main theme but Judge Dredd has a few pieces of awesome music & a great theme done by Alan Silvestri (Back to the Future, Forrest Gump, Predator).
Honourable mentions:
Back to The Future
Superman Doomsday (better music than the the first film in my opinion)
Stars Wars IV-VI
Pirates of the Caribbean:The Curse of the Black Pearl (Hans Zimmer didn't actually compose the first one)
Superman:The Movie
The Dark Knight
V For Vendetta