It is easy to forget that the most simple way to trouble shoot a hardware issue is to exchange a known good part.
I was viewing some pictures, and when I tried to close the pictures nothing would work. I could not even open task manager to close the program!
The last thing that I did was run a virus scan, everything worked fine before that.
I could use the keyboard to open task manager, but nothing I clicked on would work (the mouse pointer moved on the screen as I moved it.)
Could the Avira anti-virus have an issue with Vista?
I changed the batterys in the (wireless) mouse, no effect.
My keyboard works fine and is on the same reciever as the mouse.
So I got the wireless mouse from my wifes laptop, and everything worked as it should.
I was able to close the applications that where in use, open new applications, and do what I wanted.
If I had not tried swapping the mice I could have spent days looking for a driver or other software issue that was causing the problem.
Stupid mouse.

I don't want to try to make you look dumb or anything:) But maybe the base to the mouse, it can't see. This happened to me, and it so happened the base fell down below my desk.

It is the left click button.
The mouse moves fine, and the right click button works.
It is most likely a carbon build up, but I have had the mouse for a couple of years so I bought a new one rather than spend my energy cleaning the old one.
The point was not the mouse, rather that one of the easyest, and best, ways to trouble shoot is to simply exchange a known good part for the suspect part before you spend hours looking for software (driver) issues.

Ah!! great lesson:) Learn from others experiences instead of your own:)