Mesa3D broke OpenGL
 

Long story short I wanted my openGL code to compile and I was missing the includes, so I got and installed Mesa3D.

Since then all my 3D games don't run, Quake, 2k4, etc

A little about my video setup before this:

I'm using slackware's test26 kernel
I have a Radeon 9000 and was using generic Radeon Drivers with DRI(which worked pretty well if you ask me)

Any methods to reverse/fix this and keep the inlcudes so I can compile stuff?

Here's an exerpt from Quake:

***********************************************************
You are using software Mesa (no hardware acceleration)!
Driver DLL used: libGL.so
If this is intentional, add
"+set r_allowSoftwareGL 1"
to the command line when starting the game.
***********************************************************
...WARNING: could not set the given mode (6)
Initializing OpenGL display
...setting mode 3: 640 480
Using XFree86-VidModeExtension Version 2.2
XFree86-VidModeExtension Activated at 640x480
Received signal 11, exiting...

Not sure how the Xorg built-in drivers work as I've always used nvidia but I can give you some suggestions. If you're using fglrx then this advice would probably definitely apply to you.

Installing Mesa alongside another driver that provides it's own libGL can cause issues with Mesa overwriting the libGL symlinks with it's own. Check the output of:
and see what you've got and where links go.