for me it is kingdom rush.

https://www.youtube.com/watch?v=Bpt6reSLLFs

i meant web based flash games!

Machinarium. Not even a contest! :P

I don't play flash games that often but I think I'd have to go with curve fever on this one. Multiplayer awesomeness!

Everyone thing on the old school Newgrounds.

http://www2.warnerbros.com/web/arcane/home.jsp

Based on the Cthulhu mythos, this is probably one of the best flash games I've ever played.

There's eight parts on the first adventure, four on the second. Up to a totall of twelve parts, each one can take you twenty to fourty minutes, which makes it a pretty long game for a flash!

Best commercial flash game: Machinarium

Best free flash game: What makes You Tick?
http://www.lassiegames.com/games/wmyt/

While technically true (Machinarium is indeed developed in Flash, although it's stand alone), I think OP meant browser-based flash games. That said, extraordinary game, waiting patiently for sequel (though Samorost 3 will more than suffice).

OT: Fireboy and Watergirl series are probably my favourite flash games for last 5 or so years, they are single player co-op (left hand/right hand controls individual characters), though you can play them as regular co-op with someone else, specially if you make them self-contained and use something like JoyToKey to enable gamepads.

I always loved Megaman Polarity and A Koopa's Revenge