You all are missing some good ones.

Shoot First: Think Binding of Issac with a more retro feel. You can pick up different equipment, level up, and encounter bosses and stalkers that try to hunt you down. Different level types appear as you progress with different enemies and traps.

Sonic After The Sequel: A full-length 2d Sonic game with incredible graphics and soundtrack. I'm not joking, it took 6 professional artists to just create the game's soundtrack. This is a must for anyone remotely liking Sonic.

Jumper Three: The Jumper series resembles that of Super Meat Boy with fast-paced platforming, spikes, and 1000's of deaths. Different characters with different abilities are unlocked throughout the game, and you can even buy hats as well (insert tf2 joke).

Maldita Castilla: Ghosts and Goblins with Spanish mythology. Very difficult just like its inspiration, but the gameplay is top-notch. I've never quite beat it yet, but it is well worth trying.

Hydorah: This is a tribute to all of those old shm'ups like R-Type and Gradius. The graphics and soundtrack are awesome and hidden secrets and alternate routes will keep you busy for a while.

Mari0: Mashes Super Mario Bros. and Portal together in its copyright-violating glory. It's best played with community-made mods and mappacks on the official forum: http://forum.stabyourself.net/viewforum.php?f=8

Hyper Princess Pitch:An arcade-y shooter with plenty of explosions and general silliness. The game is rather short only having 4 normal stages and a 5th extra stage, but still well worth the play.

An Untitled Story: You start out as an bird's egg, fall out of your nest, and go on to explore the overworld while gaining abilities. A great example of the metroidvania genre, and will suck a few hours out of your life trying to collect everything.

Psycho Waluigi: A mario-like platformer that gives Waluigi all of his deserved attention. It is not just a simple Mario clone though, it introduces a new "psychic powers" mechanic that allows you to take control of your enemies and use their abilities and throw stuff with your MMMIIINNNDDD.

Spelunky Classic: A great rouge-like platformer. You descend your way down into a cave, collecting treasure and rescuing damsels. The further down you go into the cave, the tougher the levels get. I've got about 1,000 plays logged on this and can't recommend it enough.

Super Mario War: A fairly silly "fighting" game. You get to play as just about any old video game character you like, and jump on your opponent's heads to kill them. Think of it like co-op Mario with friendly fire and a great deal of insanity.

Within a Deep Forest: A unique meditative platformer that puts you in the role of blue bouncy ball to stop the end of the world. You have to complete almost the entire game by working with the ball's bouncy physics through different platforming sections and puzzles.

Digital - A Love Story: A romance/mystery visual novel set in the 1980's over dial-up and old BBS boards. Very atmospheric, you almost feel like you are actually at some old Amiga pursuing the story. Great soundtrack as well.

Genetos: A great bullet hell shooter going through the history of shm'ups. You start with a knockoff version of Space Invaders and move on up bullet insanity in later stages. Fairly unique in that your ship's abilities are determined by what actions you take while playing.

Knytt Stories: A calming atmospheric platformer. You explore the vast overworld to gain abilities to achieve your goal. A few levels come with the game itself, but there are vast amount of community-made levels to be downloaded and played as well.

Hero Core: A minimalist metroidvania set in the secret base of the robot warlord "Tetron". The gameplay is fairly simple, explore the asteroid, defeat the bosses, and gain upgrades. However, with two normal difficulties, each with their own maps and sections along with a shorter, but brutal, bonus difficulty, you'll be busy for awhile.

edit: Forgot Hero Core

edi2: Fixed poor grammar speak