Hmm... This is tough. Especially with the grey area that is the Advance Trilogy. Do those count as either Classic or Modern, or just one or the other? If the Advance Trilogy counts as Classic, then I'd probably go with Advance 3 for my Classic pick. Otherwise, probably S3&K.
For my Modern pick, it'd have to be Sonic and the Black Knight. No question.
When it comes to Classic Sonic, CD JP and Mania have to be at the top for me, although both S3&K and Chaotix wouldn't be too far behind them.
With Modern Sonic though, that's a tough thing to answer. Almost all of the soundtracks to come from the Modern era are filled to the brim with great stuff, but some soundtracks I'm particularly fond of would be Rush, Unleashed, Black Knight, Colors, Runners, and the Adventure games, that is if they even count as Modern Sonic games.