You are, of course, the director, so the final call is up to you, but here's how I think the song spread should go:
Colosseum series: 5 songs
Agate Village
Pyrite Town
The Under (Colosseum exclusive)
Pokémon Lab (XD exclusive)
Normal Battle (Story Mode) (Colosseum)
*BONUS* Pokémon Center?
Mystery Dungeon series: 5 songs
Town Square (Rescue Team)
I'm not the best person to choose PMD songs to suggest. Tuberz, TGH, would either of you two like to complete this list?
Pokémon Stadium series: 3 songs
Mewtwo Battle (Stadium)
Pika Cup Rounds 1-3 (Stadium)
Mini Games (Stadium 2)
*BONUS* Quiz (Stadium 2)
Pokémon Ranger series: 3 songs
Go-Rock Quad Encounter (Ranger)
(Again, not the best guy for this one. Someone else?)
Pokémon Puzzle series: 2 songs
Before choosing songs, we should find out if most of the music is okay. If not, there are a few original themes that didn't source from the anime.
Pokémon TCG: 2 songs
Title Theme
World Map / Mason's Lab
Pokémon Pinball series: 2 songs
Bonus Stage: Gastly (Pinball R/B)
This song
Other games: 8 songs
Pokémon Channel: Outside
PokéPark Wii: Meeting Place
Pokémon Rumble Blast: The Battle Royal
Pokémon Snap: Medley (Intro, Oak's Lab, Course Select, Camera Check)
Pokémon Trozei: Normal Stage
Pokémon Dash: White Cup
Pokémon Typing DS: Main Theme 1
Pokémon Conquest: Main Theme
*BONUS* Beach (Pokémon Snap)
Total Tracklist: 30
(Bonuses excluded from total tracklist)