With our 2003 installation.. we have things going to the data stripe on d:\program files\etc... Is there any reason not to do the same with this new install of 2007? I think it is possible to move the mailboxes after it installed (to C: \program files then move the mailbox databases over to D later on)?

I usually leave my application files on the program files root. I then move my transaction logs and databases to other directories. its not like you can really restore the program files dir anyway. and most of the performance issues are related to your transaction logs and/or databases.