I just don't like doing things the right way, OK? The right way is boring. You don't learn anything. It's... it's just too easy. So I refuse to use iTunes with my new iPod shuffle (a Chronicka gift) (Chronicka is my new Christmas-Hanukkah Portmanteau). I also dislike iTunes' harsh treatment of my carefully named and organized files (I have a huge "electronica" directory -- in a perfect world, my music would all have quality idv3 tags and I wouldn't need that, but seriously).
So I'm using gtkpod on Linux and winamp on Windows. gtkpod works perfectly, but doesn't seem to automatically transcode my ogg files (not that winamp is doing that well, but I think once I get the LAME mp3 encoder working it should be better), and while it manages the Shuffle's playlist correctly, the interface is a bit kludgy for moving whole groups of songs around on the playlist. Even with multi-select, it only moves one song at a time.
So back to Winamp, both for my larger media collection (though that's transferable, at least temporarily, using my external HDD), as well as for a slightly less grumpy interface.
Winamp's built-in portable media plugin, however, is limited in what it can do. I mean, it's powerful, has an autofill based on playcounts/ratings, syncing, and so on .... but it can't create a customized playlist order -- everything goes in in alphabetical order by file name. Uh.... Not ideal at all.
Replacing the built-in iPod support with ml_ipod, an open source, higher-functionality version, basically just fixes this.