Chrono Trigger has, in my opinion, the best soundtrack of any game I've played (and I personally consider it to be the best video game, period, in no small part because of the soundtrack). Not only does it have great songs, it's songs are consistently great. While some stand out more than others, I cannot say that I dislike a single track. Corridors of Time in particular is a track I will never get tired of for as long as I live. Metroid Prime and Super Metroid have some excellent tracks (Norfair and it's redux and Phenrana Drifts spring to mind).
Secret of Mana's music is either delightfully upbeat, perfectly frantic or incredible ambiance. Incredible game with music that fits it like a spandex bodysuit. The Fallout games do an absolutely excellent job capturing the 50s-esque pre-war era. Megaman X. Especially well done by a certain Smooth McGroove. Lastly, the Zelda series has graced us with so much amazing music over the years. To name a few: Farewell Hyrule King, Dragon Roost Island, Temple, Clock Town, Tal Tal Heights, Stone Tower Temple, Song of Healing.