At that time there was the Xfree X11 implementation, before the Xorg coming, and you had to create your configuration for your GPU and monitor combination, using scripts or from scratch, the famous Xconfig. I recall the scary warning in the documentation to not mess with your monitor modelines as you could literally burn your CRTs; monitors at that time were already equipped with builtin protections, so wrong config would only result in a black screen, but every time it happened I held my breath.
There were already at that time a lot of different window managers, like FVWM, TWM and at least one or two desktop environments. I think CDE was already available for Linux in 95...