The Mega Man cartoon shows (or “Mega Shows” as I affectionately call them) were created for and aimed at the American audience. For this reason many things were altered from the original games that they were based upon. For a full list, you can see the commentary. In fact I highly recommend anyone who has never seen the cartoons at all to at least browse the differences list before going further or you will be beyond confused.
The listings below are in the order, roughly, that the shows were aired where I lived. This is not necessarily the order in which they were made, and also I’ve taken some liberties with the list (for instance, the station where I lived showed “Electric Nightmare” first, but I figured “The Beginning” ought to be placed on top). Additionally, I’m not completely sure about which seasons some of the shows belong in, since as I said, the station around here wasn’t necessarily consistent.
Note: In the guest appearances listings, I don’t mention Proto Man, Guts Man, or Cut Man, because they’re in every episode.
As an interesting aside, if you want to see how the shows could have been, check out the promo page!