Which software to choose really depends on what you want to do with the STLs once you've got them collected together. I'm guessing that anything that imports an STL will also allow you to move it to some selected XYZ position and orientation. So if you only want to look at the collected bones, then I guess any software that imports STLs will do.
If you want to do mechanical things (e.g. rotate relative to each other) with them, then try a CAD program like OnShape.com or OpenSCAD or FreeCAD.
If you want to do deformations, then something like MeshMixer (maybe Blender) would be good, I guess.
You can convert many STLs into something more useful (useful depends on what you want to do with them) by importing into FreeCAD.