I tried using Linux alternatives to iTunes, but it was always a pain. Even iTunes itself on a separate windows box was more of a hassle than I wanted. I eventually discovered rockbox, which works great with my iPod (5th gen AKA video): it has way more config options and allows me to simply create .m3u playlists and use my own folder structure. If your iPod is supported (www.rockbox.org/wiki/IpodPort.html), I’d absolutely recommend Rockbox over other solutions.
If your iPod isn’t supported by Rockbox (like my nano 5th gen), you could probably use strawberry or GTKpod. Both are imperfect, but work “good enough”.
Now there’s a name I haven’t heard in… 15 years. There was even a build you could install on the iPod to give you a completely different user experience there.
Edit: looks like Brie linked to it in another comment. I liked it as an iPod OS, was more intuitive to me.
Amarok has support for managing music on iPods. Rockbox is an alternate operating system which doesn’t use the iPod’s database, and instead does its own indexing.