Done Right: Secret of Mana (SNES). It flows though and helps set a good atmosphere, only going full ham when it needs to. A lot of the time, it helps carry players though tougher areas though the serenity of the calm tracks.
Done Wrong: Most anything using the Mega Drive's GEMS engine. This means most western developed games. Documentation was
scarce at best for it, so more often than not, what you ended up hearing sounded akin to Mystic Cave Zone after several helpings of refried beans, a perfect fit for the grossout culture of the 90s.
Done Wrong: Most of Final Fantasy IV DS. While I'm going to be wrong and say that FF4 didn't have a strong soundtrack to begin with, the remake didn't help matters much at all. Some of it follows the weak compositions too strongly, some of it goes out of tune, and others just are a bit off as all.
dtgreene: I'll look at the Sega Genesis Phantasy Star games here as my example, mainly because they're the most interesting case I can think of off hand.
Phantasy Star 2: Done wrong. The music in this game is just not that good and not that interesting.
How can you loathe the soundtrack of a game whose primary instrument is a snare drum? :p