I absolutely love the music in the Mystery Dungeon games! :) A lot of them are very powerful emotionally. They're probably largely responsible for my huge appreciation of video game music in general. I like too many, but off the top of my head, here are some that I especially enjoyed:
Rescue Team:
Great Canyon, Fugitives (that theme that plays as you're running away from everyone), Sky Tower. Huh, I don't think that's all.
Explorers of _:
Treasure Town, New Home (that one in your partner's home in Sharpedo Bluff), Brine Cave, Far Amp Plains, I Don't Want to Say Goodbye, Dialga's Fight to the Finish, Memories, Sacrifice, Sky Peak (Forest, I think), Dusk Forest (the one in the future that sounds frantic), Defend Globe, Barren Valley, Temporal Tower, Vast Ice Mountain, that Igglybuff explorer theme, and Random Dungeon Theme 3. O_o That's a lot more than I thought I would put down...
Gates to Infinity:
Stompstump Peak, Post Town, Paradise (fully built-up version), the forest leading to Munna, Withered Savannah, Ochre Quarry, Scorching Desert, Holehills, the one that plays during the surprise air raid, Wrapped in a Light, Frism, Bittercold (phase 2), the opening theme and pretty much all versions/iterations of the Theme of Hope. There are plenty more, but I need to listen to them more. :P