Small changes were made to the Saturn V launcher over the course of the program -- for example, redundant ullage rockets were deleted, reducing the mass of the interstage between first and second stages from 12,436 lbs on Apollo 8 to 9975 lbs on Apollo 17.
As Uwe notes, the propellant loading on the second stage is the most obvious difference flight-to-flight; the stage would be loaded with enough fuel to perform the mission, plus a safety margin, but no more.
There was a small revision to the fuel injectors in the first-stage engines that was intended to improve performance, flown on Apollo 15-17, but the difference was a fraction of a percent, in fact less than the variation between individual engines on a single rocket.
Up top, the descent engine nozzle of the lunar module was extended slightly on the later missions, which yielded slightly more thrust, and the fuel tanks were enlarged. On one mission, the longer nozzle was actually damaged when it touched down on uneven ground, but this was inconsequential, as the descent stage was done with its job at that point.