Here's a list of 100 indie games that I've enjoyed. This list includes freeware games, shareware games, japanese indie import games, mods, and works in progress (WIP). It does not include browser games. I've tried to spread different genres more evenly around in the list so take the order as more of a general idea of how they rank than an absolute win/lose situation. This is not an exhaustive list and I encourage anyone with games that I forgot to post them in the forum.
For old Dos games, I suggest using Dos Box. Some of these games come in .rar or .lzh format and if you can't open them, try the freeware 7-Zip. Some of these games are japanese and need to be downloaded through a website called Vector. Here's a handy-dandy graphical guide to navigating that site.
#100 Cosmic Invaders Direct Link (Freeware)
Tower Defense meets Space Invaders. The combination works suprisingly well.
#99 Typestriker XE (Freeware)
An odd attempt to mix Shmups with a typing tutor. Flawed, but still fun. The game was originally shareware so you need to enter this key to unlock the full version features.
#98 Red Ace Squadron Pro (Shareware)
WWI "lite" flight sim with multiplayer capabilities. Designed to be played with the mouse and keyboard. Fun in small doses.
#97 Harpooned (Freeware)
Shmup with a social conscience that wisely uses satire instead of preaching.
#96 Progress Quest (Freeware)
Fuck MMORPGs. This is all you need.
#95 Space Hulk (Freeware)
A computer adaptation of the Space Hulk board game. Space Hulk mixes the movie "Aliens" with the Warhammer 40K setting with awesome results. It's like a coffe-break sized game of X-Com just as much tension between turns. This renders the original #95, Spacehulk SP, obsolete and really belongs higher on this list.
#94 Star Monkey (Shareware)
Old Raiden-alike with a gradius-style upgrade bar that has actual strategy to the upgrade paths. Only 3 levels, but they're huge levels. The sound effects are excellent.
#93 Juno Nemesis Remix (Shareware)
Low-Key Tempest-alike with smooth mouse controls.
#92 Ancient Domains of Mystery (Freeware)
Roguelike with an overworld, quests, and multiple randomly-generated dungeons. I like it better than Nethack because it's thematically consistent.
#91 Dink Smallwood (Freeware)
Zelda-clone with great irreverent sense of humor, though I was younger and less jaded when I last played it.
#90 Death Worm: 2-player Co-Op version (Freeware)
Be advised, however, that there are two more, repeat, two more motherhumpers.
#89 Banana Nababa Direct Link (Freeware)
Castlevania-esque game formerly called "Boss Arena." Your childhood was WASTED, weakling!
#88 Black Shades (Freeware)
Psychic Bodyguard FPS. It has really primitive polygonal graphics, but also has ragdolls, bullet time, and occasional zombie city levels. Turning on debug mode gives you force powers. Whitney Houston soundtrack not included.
#87 Grid Wars 2 Direct Link (Freeware)
Fuck Microsoft! Fuck XBLA! Oi! Oi! Oi!
#86 TUMIKI Fighters (Freeware)
Abstract horizontal shooter by Kenta Cho. Capture the wrecks of downed enemies which stick to your ship adding firepower and providing a "meat" shield. This is getting ported to the Wii under the title "Blast Works."
#85 Notrium (Freeware)
Sci Fi Robinson Crusoe game using the crimsonlands engine. Gather and combine materials to create tools and weapons. Seek food and shelter to survive in the semirandomly created planet crawling with hostile aliens. Unfortunately, the game really lost something when they added the hermit's cabin that you crash land in at the start of the game.
#84 Titanion (Freeware)
Kenta Cho's abstract take on "Galaga." The twist is YOUR ship has the capture beam. Except for "Modern" mode where you have a "provocation beam." You shoot it at the pink galaga enemies to make them fire more bullets at you. The bullets will explode in a huge multiplier chain reaction if they're touching the galaga when you destroy it.
#83 Audiosurf Steam (Shareware)
A game that turns your songs into Klax with abstract racing game aesthetics that move to the beat. The really cool thing is that the speed of the gameplay rises and lowers in time with the intensity (volume?) of the song.
#82 Spheres of Chaos (Freeware)
There are games that say their visuals are "trippy." There are games that describe themselves as "blah blah blah... on crack!" And then there's Spheres of Chaos. Put on your headphones, turn off the lights, and let this Asteroids-alike turn your brain into an omlet.
#81 One Must Fall: 2097 DOS Game (Freeware)
Giant-Robot-Themed PC Fighting Game from the Street Fighter 2/Mortal Kombat 1 era. Your choice of Pilot decides your speed and strength, and your choice of robot determines your moves. It also includes a huge create-a-pilot/Customize-Robot tournament career mode. Note that the "Speed" bar in the "Gameplay" menu will make the game run at a normal speed on your PC.
#80 Nemesis Scroll Down (Freeware)
A remake of Gradius with updated graphics and sound. The Orchestral rendition of the classic 8-bit music is fantastic.
#79 Space Tripper (Shareware)
Arcade game with nice graphics that controls like Defender. The twist is that the game plays from an overhead perspective and in later levels your hovercraft can fall off the board. No annoying astronauts in need of defending.
#78 Dark Side (Shareware)
An Asteroids-alike with really good graphics where you're skimming along the roughly spherical surface of a large inhabited asteroid, clearing away smaller asteroids and an increasingly huge and nasty array of alien attackers. Don't bother with Mission mode, Arcade mode is where it's at.
#77 Engage to Jabberwock (Freeware)
A mixture of Legend of Zelda with bullet hell shmups. Explore the depths of the dungeon fighting villainous pumpkins, battlemechs, and chicks in crotchless lingerie riding tanks.
#76 Gunroar (Freeware)
An abstract vertical shmup by Kenta Cho based on sea battles. You control a boat that can move and aim independently with a variety of different control options. Moving to the top of the screen and zooming ahead increases the multiplier and the difficulty on the fly.
#75 War on Folvos (Shareware)
Turn-based tactical strategy game with great music. Its plot about a powerful space empire taking over an otherwise worthless desert planet to secure energy resources, only to find itself mired in battle against a guerrilla insurgency just might be a subtle allegory.