Seriously, have Apple heard of rsync? Why they want to copy every single files from my phone back to the computer? I can restore the application via the AppStore, right? I think iTunes just need to save the application's SQLite database files only if they have been modified. That will definetely speed up the backup process. (Yeah, again, rsync Apple!!!!)
Before Apple fixes this problem, I guess we have to live with the slow backup process. I used to sync my iPhone 1.x with my computer mutliple times a day. Now, I may only sync my iPhone if I have calendar update (yes, MobileMe does not support subscribed calendars yet) or updating the music/podcasts.
If you are brave enough, you can hit the "x" button to skip the backup and force iTunes just to sync your other files instead. However, that always create corrupted backup archives. If you see multiple backup folders within /Users/
The other way to skip the backup process is modifying iTunes configuration. No, you cannot find it in the iTunes Preference. You have to manually modifying the system settings by typing
defaults write com.apple.iTunes DeviceBackupsDisabled -bool true
in the Terminal application on the Mac and restart iTunes. If you want to perform the backup again, issue the same command but replacing "true" to "false" (I highly recommend to do the backup at least 1 time a week). For Windows users, sorry, may be the similar settings are hidden in the registry and I have no idea where to find it yet.