Why is this necessary at all? Why does every program have its own updater, some of which are even resident? Why can't the OS just do all of this for us? Linux and the BSDs have package managers, but there's a solution just as easy for the rest/majority:

Both Microsoft Update and Apple Software Update could be modified, very simply, to read updates for additional software from signed RSS feeds, and queue them into a background downloading service (on Windows it's called BITS, I'm sure OSX has an equivalent) when they see them. There would need be no central repository; each software package installed would simply install a subscription, and a public key for checking against it. The updates would all be installed in the operating system's "update mode" that starts after shutdown, negating any worry of updating a running program. It wouldn't even need to trouble the download centers themselves—the RSS subscriptions could be torrent containers, and every PC could be configured to serve as a peer.

Now, if it were me, I'd move the Mobile App Store from iTunes to Software Update on OSX and make it into a Multi-platform App Store, and create a similar store for Windows in their own update service... but that's perhaps, as they say on the Internets, "too much win."