Why does Visual Studio run in "Always on top" mode?
I had a similar thing happen with Visual Studio being stuck as always on top. It started happening after I hit the Windows key followed by a bunch of arrow/home/end/pageup/pagedn keystrokes by accident (I had meant to use the control key).
What seemed to clear the always-on-top behavior was to select a different application (eg: Chrome), then press Windows+Home (which minimized everything other than Chrome), then press Windows+Home again. Then I could un-minimize Visual Studio, and it would no longer be always on top.
This worked with VS2010, VS2012 and VS2013 when they got into this weird always on top mode.
Edit: revised based on comment from @Nebula
Save your work, close Visual Studio, reopen it. Hit start, or debug, or hit F5.
This worked for me.
Very strange though, for months I didn't have this problem, and earlier when I started debugging, my window was behind Visual Studio's window... Thought it strange as it never happened before. Closed Visual Studio, reopened it, and viola.