There is also a little game called Decker that'sfree and pretty fun. Plus it's got all the qualities of a roguelike and it even lets you craft your own software and hardware but you better pay your rent on time ....

Surely, you can find time to complete it at least once? It shouldn't take too long as soon as you know where everything is and what to do.
(Then again, you've only played it for two hours the first time. I'd estimate that my first run took between 10-24 hours, cutting out the gaps between play sessions.)
AFAIK, everything in the UQM package is legal freeware. It's just the title "Star Control" that isn't, hence the open-source version being referred to by its subtitle.
(Okay, now it's time to talk about games that AREN'T related to my avatar.)
-Allegiance (Space combat/RTS hybrid online multiplayer title. There's a bit of a learning curve, but it's a blast!)
-Scorched3D (Scorched Earth. In 3D. Nothing more needs be said. And if you use Linux, you don't even need Wine!)
-Starsiege: Tribes (This game and Tribes 2 were made legal freeware as a means of promoting Tribes: Vengeance. Unfortunately, they ran out of Tribes 2 keys, so it's rather difficult to get a free copy of that game now. The first game has no such issues, though, and it's still fun to play-even today.)
There's a ton more that I could list that weren't mention already, but it would be a hassle since I haven't tried them all. (I wonder if it would be reasonable to link to the "Freebies for everyone!" thread on TTLG...)

Pingus - A shameless, but really, really god Lemmings clone. Available for Windows and Unixes
[url=http://www.asahi-net.or.jp/~cs8k-cyu/windows/noiz2sa_e.html]Noiz2sa[/url] A- A very simplistic arcade shooter, but really really fun and challenging - Available for Windows and Unixes, as well as Tapwave Zodiac.

WHOA... so many posts and no Cave Story yet? I'd've thought that'd be the obvious one.
And I like it. There's a reason it gets praised to hell and back. I like Knytt Stories better, though.
http://www.cavestory.org/downloads_1.php
I also like Lyle in Cube Sector
http://www.sitesled.com/members/bogo/lyle.html
OHNO! LYLE'S KITTY HAS BEEN STOLENED AND NOW HE MUST JOURNEY THROUGH THE WONKED OUT LANDS OF THE CUBESECTOR TO RETRIEVE HIS MEOWMEOW COMPANION!
I also enjoyed TAGAP - The Apocalyptic Game About Penguins. It's sorta a fun, mindless 2D Doom Cone. Very pretty 2D graphics too, with cute penguins.
http://www.tagap.net/tagap1.htm
There's also La Mulana and it's inspiration, Maze of Galious.
http://agtp.romhack.net/project.php?id=lamulana
http://www.braingames.getput.com/mog/
I think I should clarify that the freeware/indie genre I love the most are castleroids... because so few quality ones get made, even from commercial studios. There's only, like, 5 2D Metroid games, for instance.

Just realized that "The Suffering" is also available for free by now. I think I'll give it a try. I own and adore all the other Surreal games, so maybe this will suit me too. And if it does, then I'll hope they'll do a PS3 version of any possible successors.

Also try LIberated Games.

I didn't mention Cave Story BECAUSE it was obvious to a community like this. After all, it is fairly popular for an indie title.
I intend to get cracking on La-Mulana one day, though I'm worried about how long my sanity will last in the Hell Temple. (I don't want to spoil it for myself by watching a certain DeceasedCrab suffer-in fact, I've already spoiled too much for myself by inadvertently watching the Skimpy Swimsuit scene. That image of Lemeza trying it on is now etched into my eyeballs for all eternity, and I can't unwatch it.)

Deadly Rooms of Death - a devious, very difficult, very long puzzle game with support for user-generated content. Puzzles are of the spatial relationships / monster-killing variety, sort of like Adventures of Lolo to the fourth power. The freeware download is the Architect's Edition, which is actually a graphical update of the original DROD.
Blocksum - a surprisingly intense brickwell game that forces you to add small numbers together very quickly. (No, seriously, try it.)
Robotron Blitz - an excellent tweaked remake of Robotron 2084. I have this on my computer at work. :p The download is about halfway down the page.

And for any and all video game masochists out there, here is a gem for YOU!!
I Wanna Be the Guy!

Anyway the original Poster could get a list of all the ones mentioned so far and edit the OP with that list?

area 51 and full spectrum warrior are freeware now too.
//and of course TES:Arena

I can't believe I forgot about THAT game...perhaps it seems so 'given' to me now. (Probably because just about everyone records themselves playing it and puts up the videos on YouTube.)
Should any of you dare take up the challenge of becoming The Guy, let me warn you that you have a long, arduous, painful road ahead, and the first three screens are only the beginning.

Almost forgot about De Blob

I beat it... A long time ago. I'm just glad it's over... Also, this game gives an AMAZING after-feeling when completing it. Like you just lifted a huge weight off of your shoulders. Seriously.
Freeware:
Barkley Shut Up and Jam: Gaiden
Amazing old-style RPG with an odd theme.
8-Bit Killer
Another awesome FPS game in 8-Bit, however its very short.
Banana Nababa
Cool boss rush game.