At Rod Miller Guitars, our Setups include:
Removing old strings
Polishing frets
Conditioning fret board (if not painted )
Cleaning entire guitar
Inspecting entire guitar
Nut work if needed
Restring
Truss rod adjustment
Intonation adjustment
Pickup height adjustment
Tightening all loose tuner parts
Cleaning any scratchy or dirty pots
Tightening pots
Tightening strap buttons 
Adjusting string height ( bridge or saddle height )
Custom action that is usually discussed when brought into shop
Things can be added to any work order that might be specific to that instrument ..