There's this little fan sequel to Space Jam and Barkley : Shut Up and Jam that was made with GameMaker. For a free parody game it sure is well made!
https://youtube.com/watch?v=8F1cOvZ3nS8
It's an oldie but it's a goldie!
This game really is an experience. That fucking Hybrid Song/Quad City DJs track mashup is so dope. Unfortunate that the sequel is effectively vaporware.
I was very active in the early/mid-2000s freeware scene. There's so much gold from then that is completely lost to time. I've meant to look through some old hard drives and maybe rehost a few classics I've been unable to find elsewhere. Here's some older ones:
Highly recommend the games from Japanese developer "Ikiki". Some are small prototypes, and others are longer/more fleshed out. Some of his games went on to inspire the likes of Hotline Miami, etc. Here's a page with some links to his old work and some newer stuff:
https://www.glorioustrainwrecks.com/node/11090
Iji, although it's been a while since I've played it, is a great platformer with some nice visuals:
http://www.remar.se/daniel/iji.php
The Chzo Mythos, a series of adventure games from "game critic" Yahtzee. First game might be a little dated, but it's a great series with some really cool settings:
http://www.fullyramblomatic.com/5days/
Street Bike Fury. Maybe a bit underwhelming given the current tech available to indie devs, but this was really pushing what most independent developers were doing with the likes of GameMaker and other software at the time. It's a procedurally-generated side-scrolling shooter on a bike!
http://www.reloaded.org/download/Street-Bike-Fury/231/
Fiend. Nice top-down horror game.
http://www.reloaded.org/download/Fiend/337/
Honorable mention:
http://www.instantkingdom.com/notrium/ Ahead of its time in a lot of ways - a 2D, top-down survival game from 2003! I didn't dig around on the page much, but it appears there's now a price attached to it. The original might still be there for download somewhere.