I've been editing the config.cfg file to save the keymappings that I want - I've got most of them down 'Q' 'A' for left, 'W' forward, 'E' 'D' for right, 'S' for back, 'D-pad and press' for look and attack, 'shift' for jump, del (backspace) for menu, and 'c' for console, crosshair '1' for on, 'z' weapon change.
The attached file config.txt rename to config.cfg and copy it over in your
quake/id1 folder - first rename your original config.cfg as a backup like configbak.cfg or something similar.
Its not really refined, and there may be other changes that would make the interface better - anyone feel free to modify, update and post.