The game that has my favorite soundtrack is Xenoblade. The one soundtrack that really really delivers from that is Tragic Descision.
Another game whose soundtrack that I liked is Final Fantasy X and the Ace Attorney series (except for Justice for All).

That's a toughie.

Bastion, for sure, anything Final Fantasy, Megaman, Metal Gear Solid series has some stellar music.

On the flip side; the worst soundtrack must be Gran Turismo's elevator feelgood whiskey jazz in the menu's!

I love good video game soundtracks. The Legend of Zelda series, the Final Fantasy series (esp 4,6,10), Castlevania (esp SC4) are among my favorites all-time. Xenoblade has just joined that group. Worth mentioning are the ME1 theme, especially how it's used in a special arrangement at the end to signal the grand finalie and what is really going on in the story, and KOTOR1, which captures the feel of Star Wars very well.

Almost everything from the Final Fantasy, Metroid and Zelda series, honestly. A few other games like Xenoblade and Chrono Cross too. I also enjoy a lot the remixes done by the folks at OCRemix and the like.

Tie between Nier and Chrono Cross.

The Metal Gear Solid 4 soundtrack is great! Harry Gregson-Williams is the best.

Blue Dragon has amazing music

There's so many amazing video game tracks... it would be impossible to name all my favorites.

But if I had to choose my favorite overall soundtrack? That would have to be a coin-toss between Super Mario Galaxy 2 and Super Mario Galaxy. Simply amazing compositions between the two. You can't help but smile when you listen, whether your playing the actual game or listening to it on its own. Kudos.

I'd also like to give a shout out to a soundtrack I've been listening to nonstop over the past weeks/months. The Elder Scrolls V: Skyrim soundtrack by Jeremy Soule is nothing short of amazing as well.

And another shout-out to the OST's of Sonic 2, 3, & Knuckles. So many fantastic tracks for those games.

Wind Waker - All amazing songs, especially the Great Sea music.

Ocarina Of Time - Gerudo Valley is the best music ever put in a game.

Mass Effect Trilogy - Brilliant music, mainly Therum Battle, ME theme, Leaving Earth and An End Once & For All (which was the perfect music to end the trilogy and the 2nd best game song after Gerudo Valley).

Kid Icarus Uprising - Didn't expect it too have this amazing soundtrack, plus it comes with a music player so you can listen whenever you want!!

Sonic 2 - Great 16 bit music.

Sonic - Green Hill Zone enough said.

**Edit***

Final Fantasy 9 - Great music. Battle theme was great.

Journey, Uncharted, Demon's Souls, Yakuza