Dave,
Just to be clear: this is a major headache in a number of potential ways, and if you read the history of this thread, you'll see various different scenarios.
In my case, I have a LONG history of iTunes music purchases from the days before mac.com (third-party-email AppleID), and a LONG list of app purchases made with a distinct me.com AppleID.
Why didn't I tie the old account to the iPhone app store too, back in 2008? Well, there were two entirely separate Apple-run stores initially accessible only on different platforms, being used for different reasons. There had been no way around acquiring a second AppleID because of how the mac.com signup had worked anyway, and I expected the mac.com / me.com setup for apps might facilitate better integration with the iOS (partially true). And it seemed logical to use different a different credit card for music and for apps (the latter being business expenses sometimes). All perfectly reasonable at the time.
The problem is not just that only half of my purchase history can talk to iCloud, though that's a nuisance.
Worse: if I happen to plug my iPad to my computer's iTunes (which signs into the old ID so I can play all my music), the sync operation VAPORIZES my app purchases on the me.com account. And all their data. (Yes -- all their data; when I re-installed, I lost work.) Needless to say, I have since learned how to prevent iTunes from "helping me" with my iPad (plug it in with apple-option keys pressed, then disable automatic syncing for the device).
(As far as I can tell, the only solution -- if this mess goes on -- would be to buy DRM-removal software with which to CONVERT each of my old iTunes music files to unprotected mp3 files [running a virtual burn-and-re-import cycle for each album], let go of the convenience of accessing purchase-history-related features for all those purchases, start manually managing all that music as if I had initially imported it all from CDs, start signing into iTunes with the mac.com ID, and wash my hands of that older accoount. I'll let you know when I have a workweek to spend on that. Maybe Apple will spend $30 for each of us to subsidize a purchase of that third-party software to remove the DRM "feature"?)