Here's a post from iphonealley.com that offers a suggestion to solve this problem which I notice on my iPad. I haven't tried this yet, so proceed with caution.
Possible Fix for Slow iPhone, iPad Backup (Updated)
Submitted by Darren Beckett on May 15, 2010 - 12:23pm.
* iPod touch
If your iPhone or iPad is set to sync automatically when you plug it into your computer, you likely noticed it always performs a backup before syncing. Sometimes, the backup takes an extremely long time. We have found a solution that fixes most of the backup issues in iTunes.
The few steps below involve deleting your backup file in iTunes, so we recommend before you do this, make a copy of that backup file.
In iTunes, go into the settings and click on the Devices icon. There you should see your device listed under "Device backups". If you have more than one item listed, make a note of the date and time of the device backup that matches the device you are having trouble with. This will help us know which backup to make a copy of before we start removing files.
If you are using Windows, backup files are located here:
c:\Documents and Settings\USERNAME\Application Data\Apple Computer\MobileSync\Backup
Mac users will find backup files here:
In the backup folder, you will see one or more folders with a ridiculously long name, like 6de624828c9d586e1f088f932798039e57e2af7c. This is the backup file for your device. To determine which folder is the correct backup file for your device, match the date and time of the folder with the date and time you took note of above. Once you are sure you have the correct backup file, copy the folder to your desktop.
Once you have made a copy of the file, return to iTunes, go back into settings and click on the Devices icon again. In the "Devices backups" list, click on the device backup for your device, then click the "Delete Backup" button.
When this is complete, reconnect your device and allow iTunes to make a new backup. The new backup should complete much faster than before. If anything goes wrong, you can move the copy of the file on your desktop back to your backup folder.
Update: A tip was sent in that said there is a possible bug in iTunes 9.1.1 (11) that causes slow synchronization. If you re-download iTunes from the Apple site, you get version 9.1.1 (12) which supposedly solves the problem. We have not had a chance to test this, so if anyone was able to confirm this fix works be sure to let us know in the comments.