After upgrading my Visual Studio.NET 2005 installation to SP1, none of my website applications would publish. Aggravating. I started getting the hideously vague error "Index was outside the bounds of the array." Here are some suggestions on how to handle this problem.
My solution was to go into my Projects/[project name]/ directory and rename the current directory, there from my last Publish run, and then to try and publish it again. This worked for all of my projects.