Why does backing up my iPhone on iTunes take so long?
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M$2 Answers
NOTE: I am just assuming iPhone OS 3.0, will be a quick backup. I can not verify, as I have not upgraded yet.
NOTE2: If your device is jailbrocken then it will take a little longer, but mine is 2.2.1 jailbreak and it is very quick.
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M$It's possible you have a "bad app" that is asking iTunes to backup large amounts of data.
Additionally, make sure you are running the most recent iTunes and iPhone firmware version. There have been significant improvements in certain upgrades.
WWDC session
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M$