By using the Bukkit server mod, which provides a stable plugin API, it is relatively easy to add a wrapper around a scripting engine [0].
For example, a plugin providing Rhino support [2] and one providing python support [2].
I would recommend either porting your work to the Bukkit framework, or working with one of the existing plugins to include some of the cool stuff you have made.
I don't currently know what the most popular scripting plugin currently available is, but I'm sure you can find it with a bit more digging than I have done.
[0] http://dev.bukkit.org/search/?scope=projects&search=scri...