Although I did make one serious submission, I must admit it was much easier to think of Latin phrases that are, erm, unlikely to become the motto for any university anytime soon. So without further ado, the top three motto suggestions (from historical sources) for universities with an acerbic sense of humor or a more-than-healthy penchant for honesty:
Agamus igitur pingui Minerva
(‘Let us proceed with our own poor wit,’ Cicero, De Amicitia V, 19)
Opus opimum casibus
(‘A work rich in disasters,’ Tacitus, Historiae I, 2)
Ad nova tendentes semper discrimina
(‘Always aiming towards new dangers’, Walter of Châtillon, Alexandreis 9. 525)