It's really too hard to pick just one episode as a favourite, so I figured I'd go with a Top 5 which allows for a bit more flexibility. By episodes, I actually mean the half-episodes that (most of the time, anyway) the full 22 minute shows were divided up into.
For me (listed in order of airdate, starting with the earliest)... Bubblevicious It's always funny to see the cute & quiet ones finally lose it; and Bubbles is no exception. The first time I saw this episode, many years ago, by the time she'd pulled the Talking Dog out of his car (?) and started beating him in the face I was literally ROTFLMAO. Literally. I don't think that acronym even existed back then. The Bare Facts This episode deserved to win the Emmy it was nominated for, IMO. The disparate animation styles and hilarious narration by each of the girls for their parts of the story was quite a brilliant move. Possibly one of the most creative variations of the Rashomon style I've ever seen... made even more impressive by the fact this is a children's show. Just Another Manic Mojo This was another one that had me in stitches throughout. If this episode was representative of the average day in the life of Mojo, then maybe it's not really hard to see why he's completely nuts, lol. Curses, indeed.Los Dos Mojos This one is my list mostly due to how precious Bubbles is during her Mojo imitation and rantings. What's more, her success where Mojo constantly fails. Any episode that focuses on Bubbles tends to be above average, IMO; but maybe I'm biased, lol.The Powerpuff Girls' Best Rainy Day Adventure Ever Another one that just had a ton of cute & funny moments. And the Professor dressed as Bubbles... I mean it's worth watching for that alone, lol.
With special mention to Uh Oh...Dynamo, Supper Villain, Bubblevision, Super Zeroes, and Bubble Boy.
Also, since it may help (I know it helped me), here's Wikipedia's list of all the episodes.
I don't watch it anymore, but I did when I was smaller. Most of the fact I don't watch it now comes from it being canceled on my TV Box.
I had a VCR movie of the episode with Sedusa and the episode where the Mime removes all of the color from the city or something...