On the first 4 seasons of the show (1998-2002), the closing logo used at the end isn't Cartoon Network's logo (as seen on Dexter's Laboratory (1996) and many others); instead, the 1980s "swirling star" logo (as featured on Hanna-Barbera cartoons of the time, except for an updated byline mentioning Time Warner) appears.
After the credits of the 2002 season, Mojo Jojo appears inside the Cartoon Network logo and the Powerpuff Girls fly from nowhere towards Mojo Jojo.
The ending narration ("And so, once more, the day is saved, thanks to... the Powerpuff Girls!") is different in a few episodes, depending on what happened in that episode.