Thanks for the tips. I'll be buying wheel and seat locks (only like $40 from my LBS, which is much less than a new wheel). I like the idea of leaving a heavy lock and chain on my primary bike rack, will probably do that.
The anti-theft deterrent of clipless pedals has had me consider them. I want to get them for fun riding, but wasn't sure how I felt about needing to have 2 pairs of shoes with me whenever I go to campus. I'll keep considering that.