Move the Program Files folder. Using Registry Toolkit, you can type C:\Program Files in the "Search For" textbox, and type E:\Program Files in the "Replace With" textbox (or whatever the drive letter happens to be--in my case it's E). Then you can either step through each replacement, or select Replace All.
Special Note: check your registry for truncated filenames, "C:\DOCUME~1" and "C:\PROGRA~1". Any such path must also be changed to point to the new location. Use the same truncated naming convention.
After you have moved the Program Files folder and completed the registry editing, restart the computer. After a successful logon as Administrator, logoff and then logon as the next user in the Documents and Settings folder. Open regedit (or Registry Toolkit) and check for and correct any incorrect paths. Repeat for all users.
Note: After you have copied the Program Files folders to the new location, you may find that some of the old folders in the old location won't delete unless the contents of the folders are deleted first.
Logoff and logon as Administrator again, and try out your programs. If you come across one that won't run, do a registry search for the program name, and then for the program executable file, to see if incorrect path statements slipped through the process.
Some applications install themselves in their own named folder in system root (drive C:\). These can also be moved, as well, using the same techniques and registry editing.