Binding of Isaac is a fantastic game. The theme may be a bit strange and the graphics aren't anything special (though I do feel the graphics suit the gameplay), but the gameplay is top notch. In fact, I bought this bundle specifically for the Binding of Isaac DLC.

Machinarium was a flash game too and yet it is still a great game. Being a flash game doesn't necessarily mean the game is not any good. I do understand what you mean though - if it looks like a basic flash game, then perhaps its as shallow as the masses of flash games you can find on the web, but in this case its simply not the case.