I only wash the ones that are really dirty -- I try to brush or wipe them off first, though. If I have to wash them, I keep them separate and use them first.
I don't wash my eggs. My kids are "on top" of the egg gathering they check every hour all day everyday, so the eggs aren't in there long enough to get dirty.
If I do get a dirty one then I just take a paper towel and wipe off the mess i fI am going to give that egg away. If not then I just clean it before I use the egg.
If you wash the eggs then you wash off the protective bloom that is on them to keep oders and other stuff from seeping threw the shell.