You have a good point. I've asked a few friends (both graduate students, and not) and it seems to be consensus is that I should contact the department. It's been 3 months, so it's time for the moment where I ask them what's going on.
I have decided to take the graduate college's advice. You are very right that I probably should have contacted them earlier. I had refrained from doing so because I had not graduated yet, and the professor over the program I applied to I was working closely with, so I didn't want to press and make things weird between us. I do need to find out, because as I apply for jobs I find myself feeling anxious like "well, my luck is what I'll take a job back home and then grad school will give me their response." I thank you for your feedback. Now I have to figure out how to construct an e-mail that asks what I want to know, without sounding too pushy...