I apparently missed this thread, but I wanted to add my 2 cents. I was on the GameTunnel round up crew nearly 3 years ago, so we ran in to much stuff the current maturing Indie Games movement seemed to miss. I know GameTunnel is a bit of a taboo around here, but whatever, you're missing out.
I'll try to save you the effort of digging through the archives. Here's a handful of personal picks that aren't on the front page list, with brief descriptions why they should be.
Mexican Motor Mafia - A top down car "arena combat" game very much inspired by Death Rally, with a classic Mexican themed "crime lord killed my brother" 'esc story. Classic. If you're unfamiliar with Death Rally, it's like the oldskool Micro Machines racing game, but with guns. I'm not a racing game guy, and this isn't a racing game. It's a combat game with car like controls, upgrades, weaponry, and such. Excellent.
Land of Legends - The graphic have it's good and meh points, but the game is great. A fantasy Advance Wars 'esc game, with many races, and each race has their own abilities. To be honest, if you like strategy games, you should play it.
Jets N Guns - A beautiful game. Side view SHMUP. From the great atmosphere of a rock soundtrack, to all the subtle details of people running along the landscape being crushed by crashing/exploding enemy ships. I'm personally torn between this and Tyrian as my favorite SHMUP.
UltraTron - Alright, I love Puppygames's work. Their latest stuff all has this awesome minimalistic look, with great atmosphere and audio. The best way I can describe their work is, as good as your memory of how much you loved certain older games. Of course, when you play many older games, you realize many places they actually suck, but I'd say the Puppygames titles capture that vibe and modernize it. Anyways, Ultratron is your Robotron/Llamatron 'esc arena shooter. Two sticks of control, one for movement, one for your gun. It's probably too difficult for some gamers, but it captures the vibe.
Titan Attacks - Puppygames awesomeness for the masses. An arcade single screen shooter. Very nostalgic.
The Mastermind - This was actually a very buggy game when I reviewed it, but I really *really* enjoyed it. I imagine it's been lost in obscurity, but I really had to bring it up again. You play a criminal mastermind trying to build your crime empire. Excellent.
Weird Worlds: Return to Infinite Space - Dude. I love this game. Conquer the universe in about an hour. Space combat, strategy, trading, fantastic atmosphere (Coffee? Copy that. Napkin? Roger), I don't know what else to say. I love it.
Virus (From Tamestorm) - It's probably a really short list of people that liked this game, but I think it's something special. It's a sort of computer network/virus RTS. It's very simple to play, all clicking with simple tweaks, as you amass a large virus army to take over the network. Sure, it's not pretty, but IMO notable.
Magic Blackboard - Back in my day, we were amazed at how many people opted to make breakout/arkanoid clones for the casual games market. There's a couple I think are notable. This first one, Magic Blackboard is wacky. It features fullscreen blur, and oddities such as what I call the "space gator". I know a lot of people thought Plasma Pong was wacky, but they haven't played Magic Blackboard. You just have to see it. It's a breakout/arkanoid, but it's crazy.
BreakQuest - Number two for our breakout/arkanoids, BreakQuest. It's exactly what it is, but it's physics and theme crazy. Each level is a completely different challenge/theme. Not just lame ass different block arrangements. Many have different rules, like a centipede themed one, and so on. If there's an ultimate or winner as far as creativity among the assault of breakout/arkanoids, it's BreakQuest. Few games are this diverse.
Cactus Bruce - An oddball game. While the round up was full of breakout/arkanoid clones in my day, this game took the perspective and did something different. Given a breakout'ish puzzle, you have a stationary extendable claw that can grab things, and throw them. In some situations, the claw acted like a shield too. A very neat game.
Little Soldiers - Classic DMac
. I adore this game, 'cause I was working on something like it a few years before that I never finished. Though my direction was towards an action strategy game, Little Soldiers was a puzzle game. I'm not sure how to describe it. A puzzle platformer with moves instead of controls. Each tile is a place you can move to, in a number of ways. Rockford/Boulderdash with gravity that affects the character, and no normal need to dig. It's tough to describe. Still, I think it's very cool.
Super Dudester/Super Elvis - This game doesn't exist anymore, but it was great. A Puppygames title, almost Wario Ware'esc, with a great dark atmosphere. You controlled Elvis through several rooms, playing minigames with different rules all derived from moving a character, and interacting with things in a room. Sometimes it would be "collect" the things, other times it would be kill the things, and several variations in between. This was a fantastic lost gem of a game.