My favorite goodies are similar to many already listed.
One of those metal credit card sized action & setup gauges is handy for slipping between the strings & headstock when filing nut slots.
Oh yeah, they're handy for checking action height too.
A set of automotive feeler gauges is good to have around too. They can be stacked as needed for just about any thickness.
A few different fully threaded screws for use as bushing pullers.
5/16 x 24 gets out Gibson tailpiece bushings.
10 - 32 pulls Gibson bridge bushings.
M8 x 1.25 takes care of the metric needs.
My calipers has been modded so I can get an accurate measurement of fret height.
A capo comes in handy too for keeping the strings from tangling, when pulling bridge pins to adjust saddle height on acoustics.
And don't forget my chain saw. I couldn't route anything without that...