How to always show window controls in Yosemite full screen apps?
Use Option + Shift + Click green button to get the old fill screen behavior of expand to fill the whole screen.

Use Option + Click green button to get the old green button behavior to just expand vertically.

This was also driving me nuts today since every time that I change my KVM switch to my other machine, I end up with OS X resizing all of my windows! Argh! At least now I can get them back to the sizes I want. But the windows that I don't want to take up much room are still getting moved around annoyingly.