hmmm, a tough one indeed.
In no particular order my top three are
HG/SS-These games were amazing. The graphics are amazing, the menus are amazing, and everything is revamped and improved upon since D/P/PLT. The graphics are smoother, its the only pokemon game besides the original gold and silver to have two regions, plus YOUR FUCKING POKEMON WALKS WITH YOU AND YOU CAN TALK TO IT. I never understood why this feature hasn't returned. Plus you can toggle the running shoes which is cool as well.
Emerald- Gen III overall is just amazing. Even today, ten years later this game is as enjoyable to play as it was when it first came out. The starters are the best out of the entire series, no argument, the story was great, the evil teams were kind of weak but it is still an awesome game. My first pokemon game.
Black/White- These games were great. The starters are kind of weak, I wish Samurott would be Water/Fighting or Water/Bug. Gen V introduced some of the best pokemon in the game, the story was great, N was great, though it was a bit short.