Finishing baseboards

We are in the process of touching up and finishing the baseboards that we recently put into our home. Some of the things that I know this will include are patching the nail holes and touching up the pain around them as well as sanding where two pieces meet and touching up that paint as well. My question really is how to deal with the space between the wall and the baseboard. It seems that there are two different problems. In some places the baseboard material is slightly warped and pulls away from the wall and in other places the wall is out of plumb. Should I seal the top of the baseboard with a silicone product? Do I do the same thing at the bottom of the baseboard in the bathroom? Thanks! Jon