Seconding Persona and the Xeno universe for having fantastic music. I'd like to add Etrian Odyssey, Final Fantasy, Castlevania (bar Lords of Shadow) and the Chrono series to the list, too.
As far as individual games go, NieR hassomedownrightamazingtracks. Fits the mood of the game perfectly. Journey, Bravely Default, To The Moon and Bastion's soundtracks are also some of the best things I've heard come out of the video game industry.
There's too many to list them all. We've been getting some pretty awesome soundtracks recently.
For franchises, Halo and Final Fantasy are easy choices. In terms of more recent, individual titles, with the big music update Payday 2 has a vast array of quality soundtracks to heist to!
I find the Legend of Zelda and Metroid have fantastic soundtracks for the most part. While I've always liked Zelda and Metroid music, being a musician has made me appreciate the soundtracks even more!
Okami
Okamiden
Chrono Trigger
Chrono Cross
Older Final Fantasies
Dragon Quest series
Zelda series
To the Moon
Shadow of the Colossus
Phantasy Star
Child of Light (The Hymn of Light)
Skies of Arcadia
Lunar: Silver Star Story Complete
Grandia II
There's more I can't think of...
1. Kirby
2. Sonic the Hedgehog
3. The Legend of Zelda
4. Dust: An Elysian Tail
5. Spyro 1-ETD
6. Kingdom Hearts
7. Child of Light
8. Freedom Planet
9. Super Mario Galaxy 1 & 2
10. Donkey Kong Country 1 & 2
11. Croc: Legend of the Gobbos
12. Banjo Kazooie & Tooie
Think this is all the ones I can list concerning my favorites.
Sonic CD Japanese Japanese soundtrack: Really adore it's upbeat and incredibly crazy sounding tunes. Not to mention you get 3 various version of said music as you travel to past and future.
Streets of rage: love the sound track, each level has a really unique tune from the last. Most certainly the megadrive ' s best soundtrack next to sonic.
Hotline miami: very upbeat and 80s love the music when you strike the police station. Feels like being in a cheesy action 80s movie.
Legend of Zelda (Much of the music is overused, either remixed or directly imported from earlier games)
Series that have great music but do not make the cut (in my opinion).
Starfox (Only the 1st SNES game has great music in my opinion)
Master Of Orion (Game 2 has some of the best music ever created but games 1 and 3 have poor music)
Metroid (It's more atmospheric ambience than music most times. Totally fits in with the type of games they are but it's just different so I could not include them)
Night Sky (It's only a single game, not a series but it has great music, I like it a lot)
Secret of Evermore (It's only a single game, not a series but it has great music, I like it a lot, very fun but flawed game though)
Blaster Master (Only the NES original had good music)
BreakQuest (It's only a single game, not a series but it has great music, I like it a lot)
Vanquish is one that comes to mind in terms of a single game. Oh, and Shadow of the Colossus.
As for Series, Zelda, Blazblue, Persona, Tales Of, and Animal Crossing are some of my personal favorites.