Here are my faves:
Gen I Team Rocket's Hideout - really like the sound of it, brings in a sense of danger
Gen II I have two faves here, couldn't narrow it down to one since it's such a good soundtrack...
Trainer Challenge Theme 1 - love the feel of this one, action/adventure... and Rocket Tower Takeover, it feels a lot like the anime here, and it makes me grin from ear to ear
Gen III Wild Pokémon Battle ! - like this one in terms of bringing some excitement into the battles
Gen IV Television Channel - just like the pleasantness of this theme
Gen V Unwavering Emotions - first song in the series to almost bring tears to my eyes, so emotional and well composed
Gen VI Pokemon X & Y Wild Pokemon Battle Theme - one of my favorite battle themes, just really well done
Gen VII Battle! Wild Pokemon! - thought this one was pretty good
Side games (putting them here) - from Pokémon Colosseum (love the entire OST to be honest) - Normal Battle - love this theme, it's fun to listen to; from Pokémon Trading Card Game - Club Leader Duel - love the intenseness of this theme; from Pokémon Mystery Dungeon: Blue Rescue Dungeon - Tiny Woods - just really like this theme, nice and light