While this may be a bit "off-topic" on SO, I'll say that I prefer to use Ctrl-E. Here's my script for it (that I got from somewhere else):
" Toggle Vexplore with Ctrl-E
function! ToggleVExplorer()
if exists("t:expl_buf_num")
let expl_win_num = bufwinnr(t:expl_buf_num)
if expl_win_num != -1
let cur_win_nr = winnr()
exec expl_win_num . 'wincmd w'
close
exec cur_win_nr . 'wincmd w'
unlet t:expl_buf_num
else
unlet t:expl_buf_num
endif
else
exec '1wincmd w'
Vexplore
let t:expl_buf_num = bufnr("%")
endif
endfunction
map <silent> <C-E> :call ToggleVExplorer()<CR>
" Hit enter in the file browser to open the selected
" file with :vsplit to the right of browser
"let g:netrw_brows_split = 4
"let g:netrow_altv = 1
" Default to tree mode
let g:netrw_liststyle = 3
Just throw that in your .vimrc and you should be fine.
I prefer this because it's very simple. It doesn't take up much resources and isn't computationally expensive. That's just personal preference.
Try them against each other and see what you like.
Regarding differences, I think NerdTree is more full-featured, though I'm not completely familiar with it, as I removed it a couple hours after implementing it. I just remember it taking a bit longer to respond than this.