In September, there had been some hope that Apple was working on a solution to allow users to merge multiple Apple IDs into one. The news came from an encouraging phone call from Apple's executive relations team saying that they were aware of the issue and seemingly working on it.
Now that iCloud has launched, many have been wondering if anything had come of the previous discussion. One reader emailed Tim Cook and received an official response. Apple is simply pointing users to a support document outlining your options for managing multiple Apple IDs. Unfortunately, merging is not one of the options.
Their recommended solution is, of course, to use the same Apple ID for both store purchases and iCloud. They also explicitly state that merging simply isn't an option:
Can I merge multiple Apple IDs into one?
You cannot merge two or more Apple IDs into a single one. You can, however, use one Apple ID for iCloud services and another Apple ID for store purchases (including iTunes in the Cloud and iTunes Match). See “Using one Apple ID for iCloud and a different Apple ID for Store Purchases” above for details.
The document does outline the possibility to use one Apple ID for store purchases and another for iCloud, but that's as far as it goes.