Lauren, from academic point of view the top three would be IMO (in no particular order) Utrecht, Cologne and Lund. Utrecht and Lund are small, very uni-centered towns within a short train ride to a big city (Amsterdam) resp. mid-sized city (Malmö). Cologne is a big city itself (1 mio inhabitants) and offers a lot more than those small towns but differs very much from them. It's university is also the biggest in Germany (about 65000 students).
The beer is much cheaper in Cologne :-)