If it's for performance you might benefit from packaging it into a ThinApp, but to be honest I'm not sure. I assume any processing that needs to occur will still have to occur one way or another.
Although, if you suspect services causing slowdown why not disable or set them to manual on boot? Assuming your install still works and doesn't need those services explicitly set to automatic that is.
Good luck with it though, I've heard of many problems with .NET Framework over the years.
~Brandit
