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The Epic Battle Fantasy is quite famous (really hyped about the 5, about 85% done), but Matt also did Bullet Heaven. The first one was OK, the 2nd is one of my favorite flash game ever. (he also did Adventure Story but Meh.)
Another really cool shooter is Frantic 2.
There's also Mike Shadow: I Paid For It and the Combo Factory serie, where the goal is to deal the most damages in a limited time.
If action's not your type, Rebuild 2 was really cool (you manage a city during a zombie apocalypse) and the Grow serie is adorable (you use some things one after another and they interact together, the goal is to find the right combination). My favorite is Grow Valley, Island is cool too (it was on the /f/ a few days ago)