I name each layer and organize different page elements into folders/subfolders all while I design. I rarely merge things together and when I do, I will sometimes have a hidden version thats unmerged. Then when I am going to hand the design over I will quickly go through it to make sure its nice and organized.

While I don't see this as an extra thing to charge for, usually its the talented and more professional designers who keep their files organized...so then again I guess you might be paying more anyways. I think this is similar to what enigma said.