WhirlGirl was a superhero web series that was animated with Flash and featured on Showtime's website in the late 1990s to early 2000s, beginning in 1997. It has the distinction of being the first web series to have a regular schedule, as well as being the first to have a national ad campaign around it. There were at least 100 episodes, and some are still accessible through archive.org, but many are lost (their pages don't seem to have been archived).
https://web.archive.org/web/20000815061033/http://www.sho.com/whirlgirl/ (The longest list of episodes, though possibly incomplete, is accessible if you go to this address, click "vintage," and then click along archive.org's archive dates for the page until you get to the latest one. For some reason, trying to go directly there via the Wayback Machine doesn't seem to be possible.)
https://web.archive.org/web/20010223211701/http://sho.com/whirlgirl/adventures/bmframeset_ep4.cfm (This lists a few episodes in which the series crossed over with another series.)