"These are my old strings!" (you were supposed to change strings)
Calmly explain that these are new strings, but your extensive testing unavoidably caused them to show signs of wear. Try not to giggle. (Note: giggling is to be generally avoided, anyway.)

"What?! I'm not paying for work like this!" (a repair doesn't live up to a customer's naive expectations)
I haven't thought of a good response for this one.

"You must be out of your mind. $X.xx for ___ ?!" (thinks the price is too high)
Point out the quality (if possible) of your work, and politely ask if this fine instrument deserves less than the best care. This implies that what they're seeing is actually decent work. (See above note regarding giggling.)

"Hey! It used to play better than THIS!" (you had to jack up the action to stop buzzing)
Explain that, regardless of how it felt to him, the guitar was set up all wrong.
Ask who did the previous setup, and do your best to discredit him. Make something up, if necessary.

"This is filthy!" (notices fingerprints, spilled glue, solder drips, etc.)
Point out that your policy is to do only the work requested, and that he didn't ask to have the guitar cleaned. Politely offer to clean it for an additional charge.

"It took you long enough." (you've forgotten about the instrument for weeks, finally get it done, and call the customer)
Explain that:
• You had to drop everything to work on some road musician's guitar
• There was an important Repair Guy seminar, convention, or something
• Unexpected complications (suggested by a doctor - can also justify a padded bill)
• You had to order parts (suggested by an auto mechanic)
• Quality work can't be rushed