Hal Jordan, Green Lantern poster child, underwent a psychotic turn into a being that wanted to reshape all of existence. Later explained and Retconned, but still heavily controversial.
Cassandra Cain to a lot of disapproval. After spending 76 issues delving into her extraordinary psychology and fleshing her out into a complex character with high moral standards, DC tore her down and made her into a drugstore-variety Dragon Lady who started killing people like roaches. Now, they've very "cleverly" revealed that she was actually brainwashed by Deathstroke the entire time.
Mary Marvel provided an interesting contrast as a Golden Age teen amidst modern comics characters. Unfortunately DC decided to make her turn evil. Her clothes even turned black.
And her skirt was just as short as Supertorso's "Belt with a trim" microskirt after the switch! Bad move all around... then the next outfit made it look good.
In a particularly bad example of Executive Meddling, DC planned to turn Captain Atom into supervillain "Monarch." When readers guessed the plan ahead of time, they changed their minds at the last minute and made the character "Hawk" murder his partner "Dove" and don Monarch's armor. Then, in a series of decisions years down the line, they effectively reversed it, giving Hawk the new handle of "Extant", putting Captain Atom into Monarch's armor and creating a new Hawk and Dove team.
Name a Teen Titan. Chances are good he/she has tried to kill the other Titans at some point. Raven, Jericho, and Beast Boy (yes, even BB) are some of the more well known ones.
Mandrakk, the Dark Monitor from Final Crisis, was a Lovecraftian Horror ultra-vampire who wanted to feed on the life blood of existence itself until it had been bled dry. Saying he was the Ultimate Evil is not pushing the envelope. If what has been suggested - namely that he originally was the Monitor, the heroic mentor figure who laid down his life so the Universe might live in Crisis on Infinite Earths - is true, then this might be the ultimate FHT in comics.
Though never particularly heroic or stable, the Ultimate Hulk joined him as a member of the Dark Ultimates as well.
Sue Storm, believe it or not. She once went mad and became a villain named Malice, who was hell-bent on killing her former teamates. When she recovered, this was one of the biggest contributions to her changing her name from the Invisible Girl to the more mature Invisible Woman and Taking a Level in Badass.
Javi in Negation goes through this after Charon brought him back from the dead and convinced him that his conquest of the Negation-verse and his pending invasion of the main CrossGen universe was a good and necessary thing. Javi, a religious man who had questioned his faith even before his abduction to the Negation-verse, came to look upon Charon as a god, one in whom he could place his whole trust in, without question. He becomes a Knight Templar as a result.
In Archie Comics' Sonic the Hedgehog, the most notable thus far has been Fiona, who turned against the Freedom Fighters in #172 and joined Anti-Sonic/Scourge in Moebius (formerly Anti-Mobius).
Espio turned against the Freedom Fighters and Chaotix to join the Iron Dominion, but returned. It turned out to be a ruse, but it wasn't exactly a harmless one.
And before either of those two... Drago Wolf and Sleuth Dog.
#178-179, though it could just be a political debate in which both sides use violence instead of words.
Geoffrey St. John appeared to have one in issues 219-220, but this is actually a subversion, as it was soon after retconed that he'd actually been working for Ixis Naugus since before either of them were even introduced, making him The Mole instead.
Tigress in Young All-Stars after her death and resurrection at the hands of Gudra the Valkyrie, which was meant to explain her origin of becoming the Golden Age villain the Huntress.
Irredeemable is based on this concept with the Plutonian, a Superman-esque character, snapping due to the pressure and becoming the ultimate villian.
In All Fall Down, Pronto undergoes this in exchange for new legs as fast as his old ones.
A very big one few years ago was X-Men longtime member Bishop - after years of looking for a mysterious traitor who was supposed to kill X-Men, he betrayed them himself, for the same reason he joined them in the first place - to stop a Bad Future from happening.
In Sonic the Comic, Nack the Weasel is introduced as a member of the heroic Chaotix - but by the end of their introductory story he's sold them out to the Brotherhood of Metallix, an army of spectacularly evil robotic copies of Sonic. Admittedly a loose example, as a) he'd clearly already turned before the story started and b) the character was always a villain in the Sonic games, so seeing him as a hero first is the unexpected bit.
In Death Of The Family, Harley Quinn has gone from the Suicide Squad and joined up with the Joker. This is assuming that Suicide Squad can be considered Faces to begin with. She ends up back with the Squad once Joker is defeated, however.
Avengers Arena: Apex is the only one of the kidnapped teens who is actually willing to play Arcade's game, killing Juston to steal his Sentinel, seizing control of Deathlocket and the Darkhawk armor with her technopathy to carry out her plans, and using the latter to kill Nico.