If you apply the TFS2008 SP1 to a system that has been upgraded from TFS 2005, but the WSS was not upgraded from 2.0 to 3.0 you can get a problem that you cannot access the SharePoint portal sites due to WebPart load errors (you get an Event ID: 1000 error in the Windows event logs). This is because the TFS 2008 SP1 installs .NET framework 3.5 SP1 which causes some problems for WSS 2.0. Note this is not usually a problem for new installs of TFS 2008 as these use WSS 3.0 by default, but the upgrade of TFS from 2005 to 2008 does not force the upgrade of WSS 2.0 to 3.0 so sites that upgraded are susceptible.
Most of the blog posts suggest a removal of .NET 3.5 and reinstall of 2.0 with service packs, this is not an option for a TFS 2008 installation. Luckily there is a solution, the .NET framework family update. Once these patches are installed for the historic versions of .NET all seems OK
Thanks to Wes MacDonald for pointing me at this fix, saved me no end of headaches