There are some plugins that accept php commands, i know @MonsieurApple is working on something and there are some others out there
I'm building an online tool called BukkitAdmin which essentially allows you to manage your server via a web interface. You can check it out here -> http://forums.bukkit.org/threads/bukkitadmin-prealpha.4409/ If your curious how it works, it uses a plugin which php connects to via sockets.