I'm going to have to say everything from GSC, plus some others. I grew up on Pokemon Yellow and Gold, so every song is magical...especially GOLDENROD. CITY. That song was so ftw, it's the one reason why my GB Sounds is always on.
Pokemon Snap had pretty cool songs too, especially Valley, Cave, Beach, and Rainbow Cloud...
Frontier Brain theme from HGSS and Platinum.
Ho-Oh Battle theme.
Vs. Champion from HGSS.
Both the Wild and Trainer Kanto themes from HGSS.
The music that plays just before you battle Cynthia.
Team Plasma (B/W): It sounds like they're saying: "Wer'e a punk anarchist subculture and you know it!"
Blue (R/B/Y/FR/LG/B?/W?): The 8-bit theme is just pimp, lemme tell you. It's also because he's Gary Mofo Oak bitches! His Black/White theme sounds epic as well, but we won't know until he pops up in the game (which, supposedly is during Fall/Winter)!
Lavender Town (R/B/Y): It sounds epic, and is great for making pasta with.
Stadium Theme Song (N64): This song is simply kickass, and whenever I think of Pokemon, I hear some variation of this song. We've all heard it in the intros to main games.
Cynthia (D/P/Pt): Considering the prelude, I seriously wanted her theme to be some sort of instrumental thing, with trumpets and everything.
Lavender Town (G/S/HG/SS): I don't know why they butchered up Lavender Town. Every time I hear the beginning of that tune, I get hyped up for nothing.
Bicycle Music (All games): It makes it so painful to ride your bike if you have to hear that annyoing drivel every time. Of course, I have found ways to fool the game into not having it on while biking....
Low Health Theme (B/W): I only dislike this song because it should have been in every game, not just the two new ones.