reTune is a free utility for Windows, Linux or Mac that allows users to copy, paste and manage music from Windows Explorer, Mac OSX Finder, Konqueror, Nautilus or any other file manager to an Apple iPod. You just need to run this utility after plugging the iPod into the USB port and before unplugging it.

reTune scans the whole iPod volume for playable files, retrieving metadata (e.g. ID3 tags) from these files, and moving them to a location where the iPod can find them. The collected metadata and file names are then written to an iTunesDB file, which the iPod requires for proper blayback. It keeps a mapping file between the location where the music file initially was located, and where it is stored after syncing. When you plug your iPod back in, and run reTune, it will move the file back out of the iPod and make it visible in the OS file system.

Make sure you read this exhaustive tutorial on how to install and use this utility.

Download reTune for Windows here and for Linux/Mac (Python based) here.