While I'd agree it seems an unlikely match for Apple to buy Twitter, there are some interesting possibilities that I haven't seen discussed yet.
Apple's iPhone OS 3.0 will finally include a push data option allowing apps to receive updates while not actually running, thus allowing Apple to continue to disallow background apps (except a few exceptions of their own like iTunes and Mail) on the actual handheld devices themselves. These updates could be IM's, RSS feeds, or various other short messages.
One problem with this model is that it requires servers in the "cloud" to push the updates out to the iPhone or iPod with these servers effectively providing the background processing. And most of the small app developers selling apps in iTunes are not likely to own server farms to provide the servers for an unknown number of users. Twitter's infrastructure, though not without problems, could provide that same functionality for small developers and could scale well.
So, it might be possible that Apple would actually buy Twitter to integrate it with the iPhone's new push updates while nabbing one of the most discussed Internet brands available right now.
There may be other possibilities for integration with Mobile Me, and personally I would love to see some development to provide a centralized notification for use across a wide variety of technologies and standards such as e-mail, RSS, social media, IM's, voicemail, log entries, SNMP, and more. Twitter's infrastructure and popularity could become a clearing house to collect data from a wide variety of sources, both public and private, allowing it to become a universal inbox.