As far as I know, Fosters Home is Flash based (loosely methinks). But that's about it.
Despite looking like they are done in Flash (and with the release of Flash 8 geared to help animators, who's to say it won't change), all of Gennedy Tartakovskyi's stuff, the rest of the rubbish on Cartoon Network, half the stuff on Nick and South Park all use much more expensive software.
Bar Happy Tree Friends and Weebl of course (who got shown over this side of the Atlantic on MTV2). But they were net exclusive content. And Weebl had to be changed to Wobbl to stop them being sued by Fisher Price