MediaMonkey will sync mp3 or wav to your iPod. In fact, MediaMonkey Gold can do on-the-fly transcodes and sync FLAC, WMAL, or APE to mp3 for the iPod (or lossy wma and ogg for players that support those formats). MM doesn't currently support Apple Lossless or AAC, however.

But really, use iTunes. The greatest benefits of the iPod are the smart playlists and gapless playback, neither of which will work without iTunes AFAIK.

I use MediaMonkey to convert my lossless files to mp3 for iPod use but use iTunes to sync and make playlists. MM's Lame 3.97 mp3 encoder is much better than the one iTunes uses. V0 @ 245 kb/s sounds virtually identical to Apple Lossless on the iPod, and even on good home audio equipment it's pretty damn impressive although sometimes you can tell it's definitely lossy. Point is the iPod's sonics just aren't good enough to tell the difference through my $20 JVC Marshmallows (which are awesome considering the price). Ditch those iBuds ASAP.