Recently it happened to me, that I removed a nVidia 3D accelerated graphics card from my computer which was supported by nVidia’s driver and I wanted to switch back to the integrated graphics chipset which is supported by X.org. However the nVidia driver, which usually comes as a package like NVIDIA-Linux-x86-x.x-xxxx-pkg1.run, has overwritten some libraries and header files so that just changing the driver name in /etc/X11/xorg.conf worked for 2D modes, though OpenGL did not work because some of the X servers lbraries and header files were replaced. Furthermore there was no uninstallation procedure included in the driver package which I had (Version 1.0-7676).
Luckiliy the nVidia installer left a log of the files which were added or replaced in /var/lib/nvidia/log. You may want to delete the mentioned files manually and reinstall the x.org and mesa packages of your distribution to make sure the OpenGL libraries and headers are restored.
Afterwards the X server should work fine again – 3D including.