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Route 27 - amazing! Both in the games and the anime. Has to be one of my all time favourites. Others include
Team Rocket Encounter
Team Rocket battle
Team Aqua/Magma battle
Aqua/Magma boss battle
Regi battle
DP Pokemon Centre
Route 207 (again, great in the anime as well!)
Um, can't really remember because I haven't played gen 2-3 in ages
Anime only - Team Rocket Sinnoh Motto Theme - why do they not release this!? It's amazing! I love it so much
R/B Opening
Yellow Opening
Prof. Oak's Lab
Gary's theme
vs. Trainer
Route 1
Wild Pokemon attack
Vermillion City
Celadon City
vs. Gym Leader
Rocket base
Cinnabar Island
GSC:
Opening
New Bark Town
Wild Pokemon attack (Johto)
Lucky Channel
vs. Gym Leader (Johto)
vs. Lance/Ash
RSE
Opening
Wild Pokemon attack
vs. Trainer
vs. Magma/Aqua
vs. Gym Leader
vs. E4
Slateport City
Fortree City
Lilycove City
vs. Deoxys
vs. Frontier Brain
DPP:
Opening
Twinleaf Town
Lake theme
Wild Pokemon attack
vs. Trainer
vs. Gym Leader/E4
vs. Team Galaxy (I prefer that over Team Galactic)
Just north of Solaceon Town
Hearthome City
Eterna City
Jubilife City
vs. Dialga/Palkia
Gen 1: RBY Gym Leader Theme, S.S Anne, Lavander Town Gen 2: National Park, Olivine City, GSC Gym Theme, Johto Gym Battle Theme, Pokemon Stadium 2 Kanto Gym Leader Battle Gen 3: Lilycove City, RSE Victory Road Gen 4: Hearthome City, Jubilife City