.NET Application Updater Component

Here's an article that walks through the creation of a self-updating .Net application: .NET Application Updater Component

Windows Data Protection (DPAPI)

Here's another MSDN article that could come in handy: Windows Data Protection. It covers the Windows OS-level data encryption API.

Another Article on Background Copying On Windows

Background Copying

BITS: Write Auto-Updating Apps with .NET and the Background Intelligent Transfer Service API

BITS: Write Auto-Updating Apps with .NET and the Background Intelligent Transfer Service API