Banshee seems good, but it doesn't seem to support .epub or any other type of ebook files. I use my ipod more for reading than I do for music, so I'd really like a program that allows me to continue putting ebooks on my device.
The probably most famous application is calibre. It manages your ebooks and can sync them to your device. Unfortunately, according to the manual, it can sync iDevices only over the air, using wifi and a client app to connect to a local calibre server running on your desktop computer. On Windows and OSX you can link calibre to iTunes and therefore sync via usb cable.
To read details about the usage with iDevices, search for the term "ipod" in this manual: http://manual.calibre-ebook.com/calibre.pdf
You can find the Calibre software here: http://www.calibre-ebook.com/