The following articles and books describe topics mentioned above in greater detail. I've also left references above to technologies that (unfortunately, due to space and time) could not be covered in depth in this book. With the above text and the following references, you should be able to find any answer you can conceive of regarding assemblies, NGen, and deployment of managed programs.
"Speed: NGen Revs Up Your Performance with Powerful New Features"; Reid Wilkes; MSDN Magazine, April 2005; http://msdn.microsoft.com/msdnmag/issues/05/04/NGen/default.aspx.
Essential .NET, Volume 1. The Common Language Runtime; Don Box with Chris Sells; ISBN 0-201-73411-7; Addison-Wesley, 2003.
Common Language Infrastructure Annotated Standard; James S. Miller and Susann Ragsdale; ISBN 0-321-15493-2; Addison-Wesley, 2004.
Advanced .NET Programming; Simon Robinson; ISBN 1-861-00629-2; Wrox, 2002.
Writing Faster Managed Code: Know What Things Cost; Jan Gray; http://msdn.microsoft.com/library/en-us/dndotnet/html/fastmanagedcode.asp.
NGen Overview; Jason Zander; http://blogs.msdn.com/jasonz/archive/2003/09/24/53574.aspx.
Rico Mariani's Weblog; http://blogs.msdn.com/ricom.