I was actually planning on making a thread like this! Great minds think alike? XD
Some of my favorites are Super Smash Flash 2, Metal Gear Solid 2D: Sensible, A Koopa's Revenge, Mega Man Polarity, Metroid: AM2R, and several others.
Go play all these, they rock!
(And Metal Gear Solid 2D: Sensible was actually programmed for the GBA, You can play it using an emulator or on your GBA/DS using a flashcart, It isn't much, but I found it pretty cool).