Double check that you are a local administrator on the actual
sharepoint box. If your a local admin you should be god on the
portal. If you can't get in with your account trying using whatever
account your app pools and sharepoint services are running under. If
that does not work I have no other suggestion than to call Microsoft.

I burned a call to microsoft on this one. It took us 3 hours to find
that in IIS the application pool for mssharepointportal dumped.Didnt
say it had stopped. Should have caught that. Not sure why that
happened..so I am still working on it, but the sites are all backup.

Please share what the fix is for this one. I believe that I am running
into the same exact issue.

While we're waiting for a reply - because I don't understand what he
means by dumped. - have you restarted the app pools or even rebooted
the server ?

Yes I have. I always start with the restart apps and server.

Here is the short of it:

IIS for an individual sites should only have one type of
authentication. That was one issue.
For some reason anonymous access kept being turn on. We did
experiment with anonymous access, but the integrated windows
authentication works for our environment. So #1 turn on the type of
authentication that you need (only 1 type)for the site  you are having
issues.
Stop the iis for the individual website,
then goto application pools in IIs select mssharpointportalapppool
stop the service (wait a minute) then restart, then restart your iis
for the website.

We believe that the application of an update triggered this. We are
still testing and repatching.