Be aware of new laws:
http://www.debito.org/index.php/?p=701
(hey, official-type lawyer cats, bear in mind that the PAs ain't endorsing anything on any site linked to from this site. we just link to info. thanks!)
and automated gates at:
http://www.moj.go.jp/NYUKAN/nyukan63-3.pdf
http://kumamotopa.pbwiki.com/Overseas+Travel+Info?edit=1&new=1