The robots Wily uses are the robot leaders from Mega Man 1, 2, 3, 4, and 5 on the NES.
In one episode, three of Wily's robots pose as a rock band and hypnotize people with music. Spark Man, the leader of this "robot band", was voiced by a real life rock star - Mark McGrath from Sugar Ray.
Napalm Man appeared in the show's intro, but never in an actual episode.
Proto Man is evil in the show but was a good guy in the games. This show, along with the (confusing) plot from the video game Mega Man 5, convinced many people that the character is evil.
Eddie, the robot that gives Mega Man energy tanks, is green on the show, but was red in the games. The character was called Fliptop in the games, but they later started calling him Eddie as well. This was due to his name always being Eddie in the Japanese version, though - NOT because of the TV series.