Best: Hmm.. Well, I don't know. SMB3 and SMW both had great music for their forts/castles, but only one track per game each. SMB only had one track, though, and it did a good job of creating the creepy atmosphere Bowser's Castle has become known for.
I may have to split my vote between those 3, with an honorable mention for the forts (halfway points, if you will) in New SMB. They had some great music, and it was often fun attempting to get through the level. Also, an honorable mention to the Paper Mario series, since each game had its own set of forts/castles, which in turn had some great music for each one (often times a remix from a previous Mario game was thrown into the PM music).
Worst: I don't know if this will count, but the Bowser's Castle track in Mario Kart Wii has some of the worst castle music in Mario history. It starts out nice, but then quickly becomes the worst. If that doesn't count, then I won't vote for a worst this round.
I have a suggestion for a best/worst topic: level music (in general, not just castles and forts)