I'm not quite exactly sure of what you mean by "stub-based". There's a handful of technologies and tools involved in what I understand you want to accomplish. For the setup packages creation there are: NSIS, Inno Setup and the WiX Toolset, for example. A core technology is MSI. On the other hand, for application updates and the such, there's BITS and also some web stuff involved in updates publishing, like using an ATOM feed, for instance (your referenced Google Omaha might fit into this category).
It's only a bunch of pointers, but I hope it helps.