I particularly liked the pokemon ranger games, and also thought pokemon conquest was very good (considering I played samurai warriors for ps2/360 beforehand)
As for original pokemon games I always had a place for gold in my heart, even though crystal was my first pokemon game ever, I still played gold more than crystal. Mystery gift with my buddy from sunday school every week was something to look forward to.
I quit playing pokemon after diamond/pearl but I recently played heart gold and liked it alot since gold was my original fav. My brother had pokemon Red and I still remember doing the missingno and glitch city showoff to our friends on the school bus.
I still see ruby/sapphire/emerald as the highlight of my youth of pokemon games. It was just so cool having a secret base and being able to run and doing bike tricks! I always gave the interview guy some really forgeted up quotes too
*sigh* I need to get back into pokemon - I still have a stuffton of old cards