Following Mark Rushakoff's tip above, here is my mapping:
" vertical to horizontal ( | -> -- )
noremap <c-w>- <c-w>t<c-w>K
" horizontal to vertical ( -- -> | )
noremap <c-w>\| <c-w>t<c-w>H
noremap <c-w>\ <c-w>t<c-w>H
noremap <c-w>/ <c-w>t<c-w>H
Edit: use Ctrl-w r to swap two windows if they are not in the good order.