I had to call them when I set up my MM ID and had them transfer all my info from the old AppleID to my MM one (I had things like applecare, product registrations, etc).
I also asked them to transfer the itunes purchases/licenses but they said that they were not able to do that. Not a big deal as I don't actually have any purchases from the itunes store, only a handful of free ipod apps and one or two that I got for free before they started charging for them. For those free ones I just re-downloaded them on the new account. For the free-but-now-pay ones, I just use my old login info if needed for updates, etc.
Ruahrc