PMX Editor (Short for Polygon Model eXtender Editor) is one of those programs I've used for hours! It is the main tool I use to put my MMD Models together! I am actually using two different versions of PMX Editor for certain things.
Metasequoia 4 is a 3D modeling program that is highly compatible with PMD Models (The previous version of PMX). It has a lot of good features but I've never used it for actual 3D Modeling, I only use it for small editing and splitting materials better.