Two of my ISVs were asking about Microsoft applications which use the .NET Framework. When I had a quick look on the web I found a very good but quite old post from Daniel on this area (still very much worth a read) http://blogs.msdn.com/danielfe/archive/2004/11/02/251254.aspx
I think it is probably time for an update.
And some more...
And undoubtedly others which I have forgotten!!!