A fair few toons, as stated somewhere above, are made predomenantly in Flash. Not least of all one of my favourites, Metalocalypse (and if you analyse it, you can see exactly where the Motion Tweens kick in)
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No one program can do it all, but Flash lends itself to the speed animation that Metalocalypse demands - the episodes have an approximate turn around of a week, and considering that the lead writer also has to compose a song and voice act during that period, the staff are under pretty tight deadlines.
Cold Hard Flash, mecca for monetising Flash, keeps a list of shows using Flash as thier main animation package here. A few major web toons are on that list (Brackenwood, Xombie and H*R), but some mainstream cartoons are on the list as well (like Atomic Betty, Foster's Home for Imaginary Friends, Tom Visits the Mayor, Tek Jansen from the Colbert Report, and Johnny Test)
Flash = Serious Animation Tool. And if they have any sense, Adobe will make sure CS4 doesn't just have IK controls and AS4, but some decent animation tools and some fixed exporting options.