A couple of my favorite flash games are Dad-n-me and Mystery Of Time And Space. I wish the creators would release sequels to some of these internet classics.
The story of MOTAS sort of reminds me of Portal. Your a test subject in some kind of research facility and your goal is to escape the complex. It is a point-and-click game, but I loved the premise and execution.
Dad-n-Me is a beat-em' up style game where your dad drops you off at the park to "play" ha ha. The final boss, Sunchips was actually kind of tough too.
Also look up Divine Intervention. Your a priest stuck in a post apocalyptic rapture tasked with the duty of cleansing the world of the possessed. The South Park style animation and gore is pretty funny.
Xiao Xiao No.9 is an old school style arcade shooter with stick men. Pretty cool that one. lol