You can't change the iTunes behavior, as far as I can tell.
However, you can use a feature of NTFS to point that folder to another drive. This feature is typically called a "junction" or "symbolic link".
You can use this tool to create a junction:
http://technet.microsoft.com/en-us/sysinternals/bb896768.aspx
For example, let's say you want your iPhone backup to be D: ackup. You would do this:
1. close iTunes
2. Move the folder c:documents and settingsuserapplication dataapple computermobile sync ackup to D:
3. Extract the junction.zip to the Desktop.
4. Open a command prompt and enter these commands:
cd Desktop
junction D: ackup "C:Documents and SettingsusernameApplication DataApple ComputerMobile SyncBackup"
NOTE 1: Change "username" to match your current username, of course.
NOTE 2: I did not test the above! In general, junction points work OK, but only if programs don't mess with the linked directory (like rename or remove it). For example, if iTunes does something like delete the ...Mobile SyncBackup directory and then recreate it, it will no longer go to the D: ackups folder.