XSI ModTool is a 3d program.
If you want to work with body meshes but you require a free tool, XSI Modtool may be the way to go. A cut-down version of a larger pay program, XSI Modtool allows you to edit body meshing using the .smd file format. It doesn't handle multiple groups, so it's really only useful for editing a specific body mesh, not hair or accessories or frankensteining multiple body meshes together, but it includes certain features that Milkshape doesn't for editing. It's not really suited to beginners, but if you're already comfortable doing body mesh edits in Milkshape and you want some more options, it may be worth trying.
Use in Sims 2 Modding
Body Shop Meshing - very useful if you're using it for this type of editing above and already comfortable with a 3d modeling program, but it's not for beginners, nor is it incredibly versatile.