We were fans of CleanMyDrive when it was initially released, because it made managing multiple external drives a lot easier. Now, with a recent update, the app's even better.
CleanMyDrive 2 still automatically cleans up junk on external drives and hard drives, getting rid of service files, resource files, and other useless stuff clogging up your drives. Now, it also functions a bit more as a manager, allowing you to see what types of files are taking up space, copy files over by just dragging them over, and instantly eject all drives at once with a single shortcut. It's a little utility that runs quietly in the menu bar, but it's useful to keep around if you're working with a lot of external disks.
CleanMyDrive 2 (Free) [Mac App Store]