What is the acceptable thing to use for filling nail holes in wood trim - wood filler or do they make a special product specifically for this purpose. Also as far as the seam between the baseboard and wall - is it acceptable to use caulk and if so would it be 100% silicone or the acrylic caulk. I'm not sure whether to caulk/fill between the base shoe and baseboard/floor as in most places there is really no visible gap. Is it acceptable to leave these unfilled.

Your supposed to have an expansion gap around the perimeter and it should NOT be filled. Do a search for fillers.

Okay thanks I will check previous posts on the subject. Are you saying that the gap between the top of the baseboard and drywall should also be left unfilled?

fill that but make sure you use a paintable caulking.