Every version of OS X has featured a standalone application called Software Update that delivers updates to Apple's operating system, applications, and hardware drivers. According to Pocket Lint, Software Update is being deprecated in the next version of OS X, Mountain Lion, in favor of delivering software updates entirely via the Mac App Store instead.
After OS X Lion was made available only via the Mac App Store, it created a somewhat confusing situation where Apple's own programs were updated via the standalone Software Update application while many third-party apps were updated via the Mac App Store. Mountain Lion eliminates this confusion and makes the Mac experience more like that on iOS devices; Mountain Lion users will have only one interface to reckon with when updating software components on their Macs.
Presumably Apple will continue to deliver updates via Software Update for Mac users running legacy operating systems like Snow Leopard (and soon, Lion). Hopefully Apple will also continue to offer standalone updates on its support site so paranoid users like me can keep downloading and applying combo updates when OS X updates come out.