You know, I was just thinking of reviving this too since I started digging into my backlog again. And by backlog I mean "top rated games on Kongregate since I last stopped playing." Anyway, here are some of the better games I've run into lately:
Infinite Monkeys Bending Reality - A short puzzle platformer where you're a test monkey(s) in an experiment. Use your ability to bend reality to reach one of four endings and do some other platform game-type stuff (like collect things).
The Soul Driver - Make your getaway by reaching the Mexican border! Side-scrolling driving game, like one of them running games kinda except it's broken into segments and there's an actual ending.
Wasted Youth, Part 1 - An adventure-RPG game, you're a kid who just arrived at a boarding school for troubled youngsters. Everything seems pretty normal at first, you get to know everyone and do some quests and stuff, but then kids start to go missing and shit gets scary. As the name implies, half of a game that isn't quite done yet. ;[ I want the second part.
Paul & Percy - A straight-up puzzle game, you control two British doods who get all their biscuits/cookies stolen and set off to retrieve them. o_q Unique perspective but otherwise it's pretty standard puzzle fare, rather well-polished though. Also apparently it's an iPad game.
Snailiad - An adventure platformer, Metroidvania sort of deal where you control a snail set off to rescue his friends steadily disappearing from town. Collect power-ups, find secrets and deliver justice to the malelovent force behind the abductions!
Super Mario Bros. Flash - Not actually a Flash version of SMB1, despite what the title screen looks like. It takes elements from all the early Mario platformers and sticks them in a unique package of its own levels. More difficult than any of the official games, not on the same level as some of the super-duper-tough stuff that seem to be more popular these days though.
Nothing super amazing revolutionary but I've hit some decent stuff lately.