iFunBox is a popular storage management tool for iDevices. The program gives you USB access to the devices filesystem and if you're jailbroken you will have root access. iFunBox is a great transfer client for if you need to manually install a Cydia package or you just want to copy theme files or some other larger file to your phone and not have to deal with the slow speeds of WiFi-based SSHing.

Best of all iFunBox is free. Also, last night, the developers gave us a little New Year's present with iFunBox for Mac. You can download the Mac version here or the Windows version here.