QuakeForge's glsl renderer is meant to use quake's colourmap for a 100% faithful software look while being hardware accelerated. I've not used it myself, but the screenshots looked right.
Yeah, nearest filtering (like sw) rather than linear like glquake.
With post processing glsl and 3d textures, you can create almost any sort of colour mapping you want.
you can achieve this in fte by using the features provided by csaddon.dat - install it then just set the ca_colourtint cvar to the name of your LUT (steal one from the article I linked or something, or create one as it describes).
This is basically the only sane way I can think of applying colour distortions with linear texture sampling.
Probably you would want a slightly more polished version where everything was automatically provided by the engine itself with just an on/off setting... meh. :P
also, quake was 8-bit, not 16-bit.