SimMechanics 2nd gen has sensors built into the joints. For example if you open the parameters for a revolute joint there is a section labeled "Composite Force/Torque Sensing". In there you can have the joint block add an output port that will give you the torque.
Here's the documentation for the revolute joint: http://www.mathworks.com/help/physmod/sm/ref/revolutejoint.html?searchHighlight=revolute
