I definitely have to go with the original series here, since I grew up playing all of those as they were released. Mega Man 2 is still my favorite, with 3 and (oddly enough) 8 close behind.
Mega Man X is one of my favorite games on the SNES and I still love it to this day, but all of the sequels just didn't seem as good to me. I did enjoy playing through X4 though when I got my Playstation.
My favorite Mega Man GAME of all time? Mega Man Legends. I'm sorry, but that game was/is just so damn good. Even if it's kind of on the childish side and the bosses were easy. Legends 2 made up for that, but I didn't like it as much. It lost the charm.
Excellent voice acting and storyline! I'm still hoping for a third and final chapter some day.
I don't care for any of the other series. Especially battle network.