Don't live in Dorchester, Roxbury, or basically any part of South Boston or East Boston. This basically includes areas near the following T (subway) stops: Broadway, Andrew, Ashmont, and Mattapan on the Red Line, most of the Orange Line south of Back Bay, and most of the Silver Line Washington Street south of E. Berkeley Street. The Green Line-E Branch south of Brigham Circle is possibly not all that great either. Most grad students I know of either live in Cambridge (near Kendall/MIT, Central, Harvard, or Porter on the Red Line) or Somerville (near Davis on the Red Line), or in Boston near a stop on the B or C Branches of the Green Line.
You should also take into note the fact that Boston public transit stops operating relatively early every night: don't plan to count on the subway after 12:00 AM. Couple this with the fact that the subway system is relatively limited and that rents on places within walking distances of a subway stop are very high, and you get some people who prefer to live somewhere a bit cheaper and drive or bike to school/work (or take the bus).