Extract from Scott's blog
One of the biggest changes was that we’ve moved away from compiling everything in a web project into a single DLL (which is the only mode that VS 2002 and VS 2003 support). Instead, we now partition the web project into multiple more granular assemblies
For more details refer
http://weblogs.asp.net/scottgu/archive/2005/08/21/423201.aspx which covers
1) Best techniques for re-using user control libraries in multiple web apps with VS 2005
2) Best techniques for building a single web-site that is partitioned up into multiple nested/isolated vdirs and applications with VS 2005
3) Best techniques for using MSBuild and builder helper projects with web projects in VS 2005.
4) Best techniques for upgrading from VS 2003 to VS 2005 and what project system considerations you should keep in mind.