I saw a couple projects building 3D maps using the default RMXP editor and thought it was pretty cool, but most of them were discontinued.
They weren't too simple to use either and were pretty advanced.
While going through some japanese sites I came across this game
It also uses the default map editor to build a 3D map, and thought it was also interesting.
Though, it is pretty simplistic, using 10 pictures to put together each scene (since it's 1st-person 4-directional)