A few more:
Game Boy: Pokémon Red and Blue is the real choice, but just to mention another that's not been mentioned unless I'm mistaken, Super Mario Land 2: Six Golden Coins. Your love for this soundtrack depends on your opinion of Totaka's main theme that he arranges about seven hundred times for the game. I love it.
Favorite track: I guess "Lavender Town" (Pokémon Red and Blue); "Athletic" (Super Mario Land 2: Six Golden Coins).
Game Boy Color: Pokémon Gold and Silver. There's no better entirely 8-bit soundtrack out there.
Favorite track: I can't just pick a favorite Gold and Silver track, but two that I love are "Battle! (Gym Leader--Johto Version)" because of its killer intro; and "Battle! (Gym Leader--Kanto Version)" because of how effectively it remixes the Red/Blue track despite also being 8-bit.
Game Boy Advance: yeah, gotta go with Pokémon Ruby and Sapphire, though the Ace Attorney trilogy comes really close.
Favorite track: Again, I can't even narrow it down, but two that I really love are "Sootopolis City" and "Ending Theme." I can't even pinpoint why exactly, but Ruby was my first big game I fell in love with, so that's something.
Nintendo DS: I'm not claiming it's the best, but my favorite is absolutely Professor Layton and the Curious Village. It's dear to my heart for reasons beyond logic. A couple obscure ones that people might not otherwise be compelled to check out are Hotel Dusk: Room 215 and its sequel, Last Window: The Secret of Cape West. Lots of cool vintage jazz sound in these games.
Favorite track: "Professor Layton's Theme" (Professor Layton and the Curious Village); literally the whole soundtrack but in particular "Easy Feeling," "Slow Steps," "The Last Sleep," and "So Noted" (Hotel Dusk: Room 215).
Nintendo 3DS: It's a tricky one to narrow down because virtually every game Nintendo releases for 3DS has a stellar soundtrack. One that I don't believe any has mentioned is Mario & Luigi: Dream Team. I gush about this score a lot, because it's the most perfect soundtrack ever made in terms of complementing the game it appears in. It's a basically flawless work of art and taps into why I used to get excited about video game music before I was jaded by contemporary studies.
Favorite track: A really killer track is "The Law of Pajamaja." Really all of the area themes are incredible but that one just unfailingly makes me smile. Shimomura has the best knack for melody of any game composer out there, and her skills are on full display in this game.
