I really loved the Armadillo Knight games ! A great trilogy, but a shame it didn't go further than that despite hinting at a greater plot in the last one.
I also enjoyed the Sonic RPG franchise as well as Final Fantasy Sonic X (I've played a lot of sonic flash games, but ironically, no official sonic game ever).
I'll second Brackenwood, I haven't really watched many flash animated series aside from that.
If games count tho, I really loved the Armadillo Knight games ! A great trilogy, but a shame it didn't go further than that despite hinting at a greater plot in the last one.
I also enjoyed the Sonic RPG franchise as well as Final Fantasy Sonic X (I've played a lot of sonic flash games, but ironically, no official sonic game ever).