I'm surprised no one's chimed in to complain about AppleDouble files. I recently updated a machine that writes a lot of files to network shares to 10.7. Since 10.7 no longer supports older versions of AFP, this meant mounting those shares using smb://. All of a sudden, instead of just .DS_Store, I had a dot file for every new regular file to ignore.
God, those are a nightmare. And unlike DS_Store you cannot safely delete them. Some apps/formats store critical info in them. (some fonts and some fcp projects, at a minimum. Good thing we had backups.)
It's definitely time for these to go.