Group dispersion, reload and jam fixing speed, recoil handling... I'm sure there's a bunch of things that skill % could model.
That said, I never actually found out what was supposed to change in FO3, if you kept dumping points onto a certain combat skill. VATS %?
Vats %, damage (+55% if you brought your skill to 100.. didn't really make that much of a difference =/), and actually, I think it influences a bit accuracy too, though I actually never noticed, and that's mainly going by what the FWE modders (in the mod configuration panel vanilla it's stated to be influence more damage than accuracy and there's another setting that influences only damage and not accuracy, so it's possible to go further than the vanilla settings in that way.. and of course it's possible to go much further in the way that weapon skills actually influence accuracy, though unless they change the crosshair, it would probably be a bit unintuitive).