The only recent independent game I've been really pleased with is Cogs. You can just watch this Yootoob video to get the entire concept and gameplay mechanics. I would recommend that you like puzzles before you think about buying it, but it doesn't punish you much for being slow or crap at doing them really, and you'll easily be able to unlock the mass of content with little effort.
I like it because its one of a few puzzle games which isn't frustrating as such, just disappointing if you don't do the puzzle really fast; and there in lies the challenge. I enjoy it for the tactile quality too, and it sure does look nice.

Orpheus and Eurydice :)

Spiderweb Games make some interesting RPG's, and while they may be a bit derivative, Vogel improved the formula with the latest episodes.
Not released yet, and won't be for a while, but Age of Decadence is very promising.

I liked the idea of this game, and decided to bear with it to the end, and felt that it paid off. I guess I'd call it compelling, but I can't in good conscience ignore some of the astoundingly bad game design it contained. Because of the short form of the game it's not much of a problem, but some of the needless trial-and-error was even more antiquated than the pixel-chic art style. I thought we knew better by now
Still, thanks for linking it. I'm glad I played.

I linked it above, but it's not the same story - just inspired by it. Personally, I can interpret the ending in two different ways.

oh yeah beaten it too, it took me a while to figure out that i couldn't look back...
i think i've read somewhere that it's based on some greek mythos.

Rogue Trooper. One of the "best games no one played" I know.
Depths of Peril. It's my favorite action RPG.
Take Command: 2nd Manassas.
Startopia.
And a lot more, I'd guess...

Aztaka: mix of plataform, rpg, action...with amazing 2d graphics.
http://aztaka.citeremis.com/
Some say it already: Aquaria.
And Tecno-base: mix Deus Ex with System shock 2 (with similar graphics) and so fu**in high difficult and you got this very good game, it was made by a single person!!!
http://www.tecno-base.com/

I love the space sim games, but since I'm not a huge 3D buff, and since I do my gaming on a netbook, I like them more in 2D. I have tremendously enjoyed Space Rangers 2 (can be gotten from Impulse), which has a lot of personality and a nifty turn-based gameplay system.
I have also had a long love-hate affair with another 2D space-sim called Flatspace II, from the English developer Mark Sheeky. This one has a real-time Asteroid-like control system and has a permanent death option, reminiscent of roguelikes. Playing with permanent death on is very different and very exciting: you learn to be very, VERY careful; you become highly wary of the mistakes and accidents, such as the one that, a minute ago, killed the character you had been gaming on for a week. Never had I felt so tense playing a computer game before that. This one is also available on Impulse, though it is a bit expensive for what it is.

I thought about mentioning that one, as it's pretty good. It's certainly interesting and unusual to combine elements of hardcore shooters and hardcore logic puzzles, but the main problem is that the puzzles are so damn obtuse sometimes.
I stopped playing the game because I got completely stuck. I've tried to find help online, but there's no help to be found.

I posted this on RPGCodex before. My main issue with it was that ammo was "infinite", in that whenever you left a room and came back later on, it would respawn. That stopped me from buying the game.

I been emailing with the creator just because the difficult of some puzzles (of ALL puzzles). The "FPS" part is simply secundary, the game is for hardcore puzzles lovers...

Good choice, I really liked it.

I'll second Space Rangers 2. How could I forget it? It's one of my favorite games, and definitely overlooked.