I hate re-blogging posts from another blogger, but Brian Harry's post about the new guide for Troubleshooting Installation for Team Foundation is worthy of breaking my rule. A few months ago I was at a client performing an upgrade of TFS 2005 to 2008 and we hit a snag in the middle of the installation where the setup could not configure the SQL Reporting Services web directories in IIS. We spent 4 days on the phone with Microsoft who finally advised us to slick the server and install TFS 2008 from scratch then restore the databases. I have already seen some of the symptoms we experienced in this guide.
It also has some post installation configuration issues I have seen many times. These also pop up after service pack installations or similar events that alter the configurations of any of the supporting services.
Definitely keep this guide handy!