This is an ugly hack I came up with to layout my windows how I like them. I have NERDTree and Taglist in a horizontally split window to the left and MiniBufExplorer across the top of the screen. See http://yfrog.com/h7sg7fp

  autocmd VimEnter * call<SID>LayoutWindows()

  function! s:LayoutWindows()
    execute 'NERDTree'
    let nerdtree_buffer = bufnr(t:NERDTreeBufName)
    execute 'wincmd q'
    execute 'Tlist'
    execute 'wincmd h'
    execute 'split'
    execute 'b' . nerdtree_buffer

    let mbe_window = bufwinnr("-MiniBufExplorer-")
    if mbe_window != -1
      execute mbe_window . "wincmd w"
      execute 'wincmd K'
    endif

    execute 'resize +20'
    execute 'wincmd l'
  endfunction