I like most of the music from the games (too lazy to mention the ones I really like) but I can't stop listening to the Vermillion City music from HGSS (I always find myself flying to the city and just staying there for the music :crush.
RBY Champion theme and Wild theme
GSC Eusine's theme and the Lighthouse.
RSE Rival Battle and Pokemon League (inside)
Spin-off Colloseum Normal Battle XD Miror B and Primal Dialga.
DPPt Lilycove remix (Pt only) and Cynthia's theme.
Also HGSS National Park and Vermilion
G/S/C/HG/SS Team Rocket Encounter
G/S/C/HG/SS Team Rocket Battle
R/B/Y/FR/LG Gym Leader
G/S/C/HG/SS Kanto Gym Leader
G/S/C/HG/SS Radio Tower Team Rocket Takeover
And anything that starts playing as a result of viewing a glitched Hall of Fame in Red and Blue
Red/Lance's battle theme from GSC
Rival Battle from GSC
Friendly Battle from Pokemon Colosseum
Great Canyon in PMDRB
Mt. Blaze from PMDRB
Route 209 from DPPt
Cynthia Battle Theme from DPPt
Ho-Oh Battle Theme from HGSS
Dusknoir theme in PMDTDS
Primal Dialga Battle in PMDTDS
Fun Exploration from PMDEoS
Team Charm's Theme form PMDEoS
Battle vs Silver and its encounter :B
Encounter with Green/Blue in Gen I
Viridian Forest in Hg/Ss
Battle vs Red
Desert theme in pokemon XD
Elite Four theme in pokemon stadium
and the classic Battle theme from Gen I
Pallet Town (All versions)
Lavender Town (All versions)
Route 1 (R/B/Y)
Gym Theme (R/B/Y)
Ecruteak City (G/S/C)
Trainer Battle Theme 5 (I think it's the one that plays when you fight Raikou and Entei)
Kanto Gym Leader Theme (All versions)
Littleroot Town (R/S/E)
vs. Maxie/Archie (R/S/E)
Lance/Red Theme (All versions)
Celebi's Forest (Colosseum & XD)
Tournament Semi-finals (Colosseum)
All the music in Pokemon Puzzle League (Nostalgia~)
...and probably a bunch more that I'm forgetting at the moment.
Among routes, there's 1, 201, 215, 123, both remakes of 42 (there was one in FRLG), 29 remix, and 111-desert
For cities, both versions of New Bark, Lilycove, the original Cerulean and Celadon, Petalburg, and Violet.
For caves/forests, Varidian Forest, Dark Cave, Sky Pillar, and Distortion World.
All gym themes are great, but the GL battle music from Kanto is the most memorable. But the intended-to-be best battle music of all was Steven's, Cynthia's, and Distortion world Giratina's.
Pokemon Mansion (Both versions LG/FR and R/B/Y)
Cinnabar Island (Both versions)
Elite 4 (R/S/E)
The Under (Pokemon Colosseum)
Miror B's theme (Pokemon XD: Gale of Darkness)
Buena's Password show (G/S/C & HGSS)
Giratina's (Origin Forme) battle theme(pretty creepy, but awesome)
The Admins (Pokemon XD: Gale of Darkness)
Pokemon Tower (Both versions)
Sage/Channler battles (G/S/C && HGSS)