Defection: is a setting where travel between dimensions is relatively common, albeit only truly available to those on the larger end of the power pool, thus resulting in a lot of alternate versions of the same person.
Trey and Troy, the "bad" Dimensional Guardians from the web fiction serial Dimension Heroes often pick fights with the protagonists.
In the Global Guardians PBEM Universe, The ambitious and brutal Blackstar was thrown out of the Guardsmen, the intergalactic superhuman police force, and is now the sworn enemy of the heroic Guardsman, defender of Earth.
The Tyrants are a "mirror universe" version of the Global Guardians.
1d4chan has created an epic inversion with Brighthammer 40k, a reimaging of Warhammer 40,000 that replaces the Grimdark future of Warhammer 40k with a bright happy Star Trek-esque universe where the everything is going great and instead of war, there is only HIGH ADVENTURE. Essentially, it takes Warhammer 40k from the cynical side of the scale and slams it down to the idealistic side.
In The Cartoon Man, Simon becomes Roy's evil counterpart when the same black ink that caused Roy's cartoon transformation turns him into a mustache-twirling cartoon villain.
In Red VS Blue, we have the bigs bads of season 15, the Blues and Reds. It doesn't seem like it at first, though, because they first act genuinely polite and friendly towards the heroes, the Reds and Blues. Later on, it's discovered that Church's evil counterpart is a serial killer that plans on destroying the UNSC. His name is Mark Temple and he is the leader of the Blues and Reds. Almost every member of the Blues and Reds is an evil counterpart to every member of the Reds and Blues (Surge to Sarge, Gene to Simmons, Buckey to Tucker, Loco to Caboose(sort of), Temple to Church, Cronut to Donut). Here, we have a rare case where not only the evil counterparts came chronologically before the heroes, but also where not all of them are evil and where not all of them meet at all (Biff and Loco, despite being Caboose and Griff's counterparts, aren't really evil themselves. Also, Biff and Church both died before season 15, so neither of them met their respectful counterpart from each opposing team).