Kalinka, Dr. Cossack's daughter, only appeared in Mega Man 4 but is beloved by the fanbase and appears frequently in fan works, the various manga adaptations, and the Archie comics. Being one of the few female characters in the Classic series helps.
Splash Woman (from Mega Man 9), who has a huge fan base and has made many players robosexual. Aside from Roll, she's one of the very few female characters in the series, let alone for the Classic timeline, and the only female Robot Master in the Classic games.
Tango the robot cat only plays a major role in the Game Boy Mega Man V and makes a few minor cameos elsewhere, but his adorable design and general usefulness earned him many fans.
The Mega Man X5 Mavericks' Guns N' Roses-inspired names made them very memorable, to the point that when the original names were used in the X Legacy Collection releases fans were upset. Duff McWhalen in particular is especially popular, and most of the complaints about the name reversions are about how boring "Tidal Whale" is in comparison.
The Zero series spawned a few minor/temporary ones, like Chilldre Inarabitta and Leviathon.
Mega Man ZX Series
Girouette was almost one for the Mega Man ZX series until it turned out he was a Sacrificial Lamb. Come to think of it, he might be one anyway.
Mega Man Legends Series
There's also Tron's Servbots. Their popularity led to one being a joke character in Marvel vs. Capcom 2: New Age of Heroes, and one of Tron's super combos is summoning all 40 Servbots (sans the one following her) to Zerg Rush her opponent.
Battle Network Series
Mr. Match is fondly remembered as the introductory antagonist in the very first Battle Network game. His popularity was such that he was brought back in every following game but the fifth, although never as anything more than a strictly secondary character.
Princess Pride, although her popularity can mainly be attributed to her anime incarnation being a nice girl. When she made a reappearance in Team Colonel, her originally cruel personality was changed into the kind one which fans had grown to love.
Star Force Series
Sonia Strumm/Sky is this for western fans due to being one of the most likable and sweet characters of the cast and being actually capable of fighting semi-evenly with Mega Man. She's also, like Tron, pretty cute.
Hyde became somewhat subject to this to those who watched the Tribe season of the Mega Man Star Force anime, as he was changed from a sycophant quasi-Dragon in the game to an out-there, comic relief artist in the anime. It didn't hurt that his crowning moment of villainy was kidnapping the hero's mother and throwing her off buildings and bridges Green Goblin-style just for the lulz.