Well, Xanatos from Gargoyles often had multiple objectives, so that the Gargoyles could beat the more obvious plot while he got what he really wanted. Of course by the end of the series he'd teamed up with the Gargoyles, but I wouldn't say he'd turned good so much as he decided it was more beneficial to him to have the Gargoyles on his side than to keep doing the sorts of things they objected to.
Also, in Reboot Megabyte achieved his goals of conquest in Season 3 (though he was overthrown by the end of the season).
Oh, and while it isn't technically a bad guy winning, if you want a change in pace from the "villains committing crime, heroes stopping them" dynamic, in the old 90s "Sonic the Hedgehog" cartoon (AKA "SatAM") Robotnik already ruled the planet at the start of the series, and while the heroes had a minor victory almost every episode, it wasn't until the final episode that they actually overthrew him.