I was mucking around on my Mac (10.8; Mt Lion), picking through the preferences (matching those preferences to a newly-built Mt Lion virtual machine), when my left-click did something odd. Every other left-click I issued (on the desktop say) produced a right-click instead.

At the same time applications (like the System Preferences panel) disappeared. The applications did not close, nor did they minimize. They merely became invisible.

Turns out the solution to return the machine to normal behavior was simply tapping the space bar. Once tapped left-clicking was again always left-clicking and applications (once called from the netherworld by clicking their dock icons) stopped vanishing.

Not sure how to reproduce the cause, but have fun with that.