It's a dead heat between I Am the Doctor (the 11th Doctor's theme) and the Halo Theme - Mjolnir Mix (Halo 2 theme). Two very good instrumental tracks with enough variety within them to not just feel like a loop, plus they symbolize particularly epic moments from their respective series (both of which I love, which doesn't hurt, either - there's a certain nostalgia/familiarity factor there).
Instrumental songs just seem to have more staying power for me than ones with lyrics - maybe it's because when I play a song over and over (which happens often with songs I like), the words get ingrained in my head and I lose a certain sense of...anticipation. Or something. There are plenty of lyrical songs I like a lot, but they tend to shuffle around on the list of favorites at will. (My top pick among them right now is probably The Future Soon, by Jonathan Coulton, but it's a close race with a bunch of other songs.)