As far as the whole PT thing, I prefer only a few cosmetic mods. E.g.:
EXTERIOR:
Shaved door handles on b-bodies/a-bodies
tucked in bumpers and shaved bumper bolts
Wheels/tires (18" max)
INTERIOR:
New front Recaro-type seats, but with the OEM pattern
3-point seatbelts on hardtops
Steering wheel (something that could look OEM, like a leather TUFF)
Tilt column
OEM gauges, but maybe with a modern/diff silkscreen to them
I hate Autometers, non-OEM consoles for the most part
ENGINE COMPARTMENT:
cleaned up of wiring
cleaned up (but not flat) firewall
battery re-located
Fuel injection, turbos, superchargers.
Crossflow radiator, hydroboost PBs
SLick pulleys/brackets
SUSPENSION:
all changed up of course. WHatever you want. R&P front end, four-link or IRS in the rear.
PAINT:
OEM-looking color, but with a bit more pop?
Factory-looking stripes
Pro-touring can be done very tastefully, but can't be overdone. Otherwise it will age quickly. 10-15 years from now, people will be going "Man, that is so 2009!"