From the anime,
"Pokemon: The Johto Journeys" stands head and shoulders above the rest.
From the games, these all deserve mention XD
-RBY Route 1
-RBY Trainer Theme
-RBY Gym Leader Battle
-RBY Champion Theme
-GSC Rival Theme
-GSC Rival Theme, Pokemon Stadium 2 Remix (Lance Battle Theme)
-GSC Champion Theme
-GSC Kanto Gym Leader Theme
-GSC Kanto Gym Leader Theme, Pokemon Stadium 2 Remix
-RSE Wild Pokemon Theme
-RSE Rival Theme
-RSE Gym Leader Theme
-RSE Team Aqua / Magma Theme
-RSE Archie / Maxie Theme
-RSE Regi Theme
-RSE Elite Four Theme
-D/P/Pt Gym Leader Theme
-D/P/Pt Team Galactic Theme
-D/P/Pt Route 209
-D/P/Pt Sunyshore City
-D/P/Pt Cyrus Theme
-D/P/Pt Azelf / Uxie / Mesprit Theme
-D/P/Pt Dialga / Palkia Theme
-Pt Giratina Theme
-D/P/Pt Champion Theme
-Pokemon Colosseum Battle Theme
-Pokemon Colosseum Semifinal Theme
-Pokemon Colosseum Cipher Peon Theme
-Pokemon Colosseum Cipher Admin Theme
-Pokemon XD Battle Theme
-Pokemon XD Cipher Peon Theme
-Pokemon XD Cipher Admin Theme
-Pokemon XD Miror B. Theme
-Pokemon Mystery Dungeon 2 Primal Dialga Theme
...yes I know, long list :P