.NET
XNA
Photosynth
Office 2007 UI
Intellisense
ClearType
OneNote
Surface
XBOX Live
just to name a few.
.NET - modeled after Java
XNA - not sure what you think is innovative about this.
Photosynth - Not familiar with this one.
Office 2007 UI - aka: the Ribbon. Definitely new. Arguably bad.
Intellisense - Hardly the first. Had the same thing with Borland IDEs years before VS picked it up.
Clear Type - Developed outside MS, technique was picked up by MS.
Surface - Concept still under refinement at MS. Technology not developed at MS.
XBox Live - No idea what you think is innovative about it.