Hi David 
There was a post a little while ago about customisable faces, which might be helpful http://www.jmonkeyengine.com/jmeforum/index.php?topic=4312.0
For equipment, a common method is to have a placeholder or attachment point on the models, with a special name or some other way of finding it when the model is loaded. For example, planes in my game have gun0, gun1 etc. to show where to attach guns, and the same system is used for propellers, smoke effects, collision shapes etc.
I’m only familiar with doing this in blender, but basically you create a named “empty” object with no mesh data, and that will end up as a Node in the model. When you load the model you just search for the named child Nodes of the model, then attach stuff to them, like weapons etc. If the nodes are animated, they will move their child attachments around with them, so you can make them track with a hand for a weapon, etc.
You can also do a lot with textures, for different armour for example, although different meshes will look better.