Yes, you can run iTunes in Linux

Here's a great tutorial on how to configure Wine to run iTunes in Linux.

Wine -- the Linux emulation program that allows you to run Windows apps without running the Windows OS itself is notoriously difficult to run successfully, and tutorials like this are a great help. While there are other ways to manage music on the iPod under Linux (Amarok comes to mind), it makes sense to have iTunes as a choice.

And for those who really don't want to get their hands dirty with Wine, Codeweavers' Crossover Linux automates the nasty bits of the Wine experience and costs only $39.99. Well worth it. And there's a trial version so you don't have to fork over the money until you know it works.

But if you do want to learn the ways of Wine (and not pay anything, ever). the tutorial above is a great way to get started.

Other Windows apps that generally run under Wine: Microsoft Office, Internet Explorer and Photoshop. So if you're somehow wedded to the commercial apps over the free alternatives (OpenOffice, KOffice, Firefox, the GIMP), you can have your free OS cake and eat it, too, with Wine.