Elaboration provided where applicable.
I chose RSE for the Pokémon series, but all of them are close. They all also have their problems, but overall I like RSE the most.
A no-brainer with the tens of thousands of hours thrown at it and its custom maps (and recently, Valve's port of DotA Allstars) - not even Pokémon in all its iterations comes close. Arguably the best "casual" RTS in history with the strongest map editor and mapmaking hordes of any game the genre. Too bad it's all but dead nowadays with SC2, Dota 2, and other more recent titles robbing an already declining decade-old game blind.
One of the first video games I ever played, and a damn good one at that. Looking back, it has its share of flaws and there are countless better STGs out there, but nothing can match the nostalgia value.
KotOR II (with the fan restoration/bugfix patch)
Without the patches, the endgame is unfinished and a huge drop from the rest of the game. With the patches, it's still a bit below the rest, but it's good enough to complete the fantastic game.