The Powerpuff Girls short "Custody Battle" focused only on Mojo Jojo, Him, and the Rowdyruff Boys. Other than a brief clip from a previous episode, the girls didn't appear at all.
The classic Batman episode "Almost Got 'Im", where we just see villains discussing their failures for most of the 22 minutes. There's also "Mad Love" which was mostly from Harley's perspective. "The Man Who Killed Batman" was told from the perspective of a bumbling, small-time crook. There are a good bit of single episodes in the DCAU.
Gundam SEED/Destiny had some clip shows/show background shows narrated by antagonist characters which kind of involve how these events led to their personal convictions.