Just be aware that devices/programs that worked with iPhones prior to 2.0 won't necessarily work now. Media Monkey is a good example, great program for music (way better than iTunes) but as of yet they can't get it to sync with 2.0 firmware.
That being the case, you might be better off using QuickPwn to jailbreak your phone, install SSH, then SSH directly into the file system and copy the files to your HD. Once you've gotten what you need, you can easily reinstall the official firmware to remove the jailbreak and be back to factory.