Well, there are options in most modeling programs to name objects individually. If you do this and export the OBJ, the names should stick, then you'd see them in the group listing. What are you modeling in? If the program doesn't support this, use UVMapper. Just load in the object and, assuming you've UVmapped it correctly, select the eyes or teeth or whatever in the head you want to be seperate and assing them to new groups. Then save out the new OBJ and use that as your base for making a rig.