By "punch" I just mean all of the touch-up, nickle-and-dime stuff. Repair drywall that has been damaged since the install, adjust all the windows to operate smooth, weatherstrip any doors that need it, fix some of the items identified by the inspector, install lightbulbs that the elecrician forgot, setup the appliances, put the screens in the windows.... There's just a ton of little stuff left.
It seems like the subs get the job done to about 98% complete, and if you tried to get them all back to finish the last 2%, it would take you forever to finish. It's just more efficient to have someone take care of what's left. Some builder's might have staff to do this as part of their fee. Others do not. Make sure you ask, this could make a couple thousand dollars difference!
And as far as "misc", the builder should give you and itemized estimate, but there's bound to be stuff on doesn't fit under any catagory, but still costs money. For me this was mostly just odds and ends from Home Depot, but it came out to a sizable chunk of change by the time it was done.