I think taking a thread like this on a by-the-series basis would be a lot easier. But for now:
Favorite: MegaMan Legends 2
Visuals, voice, music, challenge, story, pyromania, lots of unique bosses, and most importantly, the Bonnes. What is not to love about this game?
Least favorite: MegaMan Xtreme 1
Bringing the X-series to GBC was an admirable effort, and I am a sucker for nostalgia, but what sense is there in cramming bits and pieces of two SNES games together on inferior hardware with virtually no original content? Attempting to write replays into the story wasn't the most seamless move, either. The capsules suck and the instruments are ear-splitting. I am, however, thankful for two things about this game. One, that it got Sensei to draw the X1 armor (which is badass beyond all sane reasoning). Two, that it spawned a sequel which is infinitely more awesome in every way.