At the TU Ilmenau we used OMNeT++ (http://www.omnetpp.org/) which had the benefit of having built-in classes for statistics collection and looking at graphs while the simulation ran - mininet doesn't seem to offer such functionality (yet?). But then it sometimes felt like omnet had too many layers of indirection and C++ was not everybodys language of choice.

Our assignments were similar, I remember doing stuff with link state and distance vector routing, implementing parts of a tcp state machine and others.