Applications to replace iTunes for iPod synchronization?
Banshee is the best I know.
Banshee 1.8 is undoubtedly the best one. You can simply install Banshee from Software-Center, then add the Banshee-Team repository (trough Software Center > Edit > Software Sources > Other Software > Add, and then fill in with ppa:banshee-team/ppa), and update your system trough the Update Manager.
Banshee will be in Applications > Sound and Video > Banshee Media Player. You can now plug-in your iPod, activate Banshee Podcast Plugin trough Edit > Preferences > Extensions, add your podcast and configure syncing in the iPhone's pane in Banshee.