i don't see why don't use mouse since it is officially supported. Quake in this way was much more strange: mlook (if you remember) wasn't there as "normal" option but only with console (or autoexec or other cfg) command. only later (and in build games before, but regarding "true 3d" games:)) mlook became part of the options. anyway...
my setup:
Move forward : W
Move backward : S
Look left : -
Look right : -
Look up : -
Look down : -
Look center : -
Strafe left : A
Strafe right : D
Jump : SPACE
Crouch : SHIFT
Primary fire : MB1
Secondary fire : MB2
Use key (activation of doors and buttons) : E
Next weapon: Q
next item: Z
previous item: X
use item R (or F?)
MB2 double click opens doors, middle button (wheel) is strafe too and double click jumps...
In times of doom i used to play with mouse only (MB1 - shoot, MB2 - move forward, MB3 - strafe, MB2 doubleclick - open). keyboard numbers to change weapons. DOOM had no other useful keys so mouse with 3 buttons was enough to control all action.
When DUKE appeared i used mouse still, but added:
Move forward : UP
Move backward : DOWN
Look left :
Look right :
Look up :
Look down :
Look center :
Strafe left : LEFT
Strafe right : RIGHT
Jump : CONTROL
Crouch : SHIFT
Primary fire : MB1
Secondary fire : Ins (it was a habbit to use MB2 to walk forward - habbit from Doom)
Use key (activation of doors and buttons) : MB2 double click.
but later "classic" WSAD introduced to Quake community. i resisted as long as I could untill I've started to play NOLF1 where setup didn't want to change any actual keys (letters on keyboard). i wanted to finish the game and got used to WSAD. later i even loved it because hands fell "more free" when on different sides of keyboard rather then my previous (arrows) setup, where arrows are right part of keyboard and a little bit more to the right is a mouse. kinda tied. WSAD and mouse is more like playing piano - free...
