Starting with this:
____________________
| one | two |
| | |
| |______|
| | three|
| | |
|___________|______|
Make 'three' the active window, then issue the command ctrl-w J
. This moves the current window to fill the bottom of the screen, leaving you with:
____________________
| one | two |
| | |
|___________|______|
| three |
| |
|__________________|
Now make either 'one' or 'two' the active window, then issue the command ctrl-w r
. This 'rotates' the windows in the current row, leaving you with:
____________________
| two | one |
| | |
|___________|______|
| three |
| |
|__________________|
Now make 'two' the active window, and issue the command ctrl-w H
. This moves the current window to fill the left of the screen, leaving you with:
____________________
| two | one |
| | |
| |______|
| | three|
| | |
|___________|______|
As you can see, the manouevre is a bit of a shuffle. With 3 windows, it's a bit like one of those 'tile game' puzzles. I don't recommand trying this if you have 4 or more windows - you'd be better off closing them then opening them again in the desired positions.
I made a screencast demonstrating how to work with split windows in Vim.