This is my Quake autoexec.cfg, more or less.  There's probably some other stuff in there too, but this is what I consider "important".  (I haven't included all the default binds, like 0-8, Esc, etc.)  If you have any suggestions for how to make it better let me know!
// main movement keys - left hand
bind a +jump
bind d +back
bind e +forward
bind s +moveleft
bind f +moveright
bind z +movedown
bind w +moveup

// mouse buttons - right hand
bind MOUSE1 +attack
bind MOUSE2 +jet
bind MOUSE3 +hook

// alternate right hand keys
// for rare occasions without mouse
bind UPARROW +lookdown
bind DOWNARROW +lookup
bind LEFTARROW +left
bind RIGHTARROW +right
bind INS +attack
bind DEL +hook

// weapon selection
bind SPACE "impulse 10"
bind ALT "impulse 12"
bind CTRL "impulse 7"

// general actions - applicable everywhere
bind p ping
bind q ping
bind o screenshot
bind f1 disconnect
bind f2 ""
bind f12 screenshot

// general actions - ihoc only
bind r rune
bind b drop
bind g holo
bind l handicap
bind i chase
bind c "impulse 98"
bind x "impulse 97"
bind ";" players
bind f3 vote-exit
bind f5 root-login

// message binds
bind y "say YES!"
bind n "say NO!"
bind k "say OK..."
bind h "say HI!"
bind u "say BOT!"
bind m "say BITE ME!"
bind . "say :-("
bind , "say :-)"
bind / "say ???"

// mouse settings
m_pitch -0.022000
sensitivity 7.0

// misc visual settings
v_kickpitch 0
v_kickroll 0
v_kicktime 0
cl_rollangle 0
cl_bob 0

// graphics settings
crosshair 1
gl_flashblend 0
r_wateralpha 0.4
r_waterwarp 0
r_shadows 0
gl_keeptjunctions 1
gl_ztrick 0
gl_playermip 0
gl_triplebuffer 1
gl_polyblend 1

// always run!
cl_forwardspeed 1000
cl_backspeed 1000
cl_sidespeed 1000

// fast console
scr_conspeed 2000

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