Can't close open windows,  Please Help

I'll have a Safari window open, with multiple tabs, I can close the individual tabs, but to close the only window left, I cannot close it. Any popup windows also will not close. They will shrink to dock, but I cannot close them. Any Help?

I was facing exactly the same problem after the 10.4.11 / Safari 3.0.4 Update. It is most likely caused by an input manager you have forgotten about. In my case it was the ancient Taboo 0.3. Go to
Library > InputManagers
and check for a SIMBL folder.
Removal of said folder & restarting Safari solved the issue. Brute force of course, you can also look into
Library > Application Support > SIMBL > Plugins
and delete the "Taboo.bundle".

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