I suspect this is far from comprehensive (that, or there's a depressing lack of cheap Bard options; I'm not counting Art @ Emerson and their $60 Lear here). But here's a few that are already listed:
BU/New Rep: A Midsummer Night's Dream. October 25. Okay, not truly a college troupe, but $20 still feels like a reasonable price.
BU: Henry IV, Part 1. October 23-26. Yes, the headline says "Henry VI," but based on the description, that's clearly a typo. This is the Femina Shakespeare troupe, who always do a great job (and as always, it's free).
MIT: Othello October 31st, November 1st, 2nd, 6th, 7th and 8th. MIT's been consistently doing amazing productions over the last five or six years. There's been enough cast turnover in the last year to make me a bit nervous, but I'm still planning on going to see how well the new kids can carry on the legacy. No price yet, but if it's like past productions, expect $12 for general public, $9 for students.
Harvard: Pericles: Prince of Tyre: November 7-9. Also free. Not normally one of my favorite plays, but I'll give it a shot.
Emerson appears to have Taming of the Shrew planned for December (but with no times/dates/prices listed yet). I'll update once info is available.
The Wellesley and BU ensemble pages haven't been updated yet, but it's safe to assume they'll have something (and I'll update the post once I find out). Brandeis's Hold Thy Peace troupe was making noises about doing Midsummer, but I can't find anything definite online yet. BC's got a couple of Spring plans (including a January production), but nothing in the fall. Nothing at Northeastern (they're choosing Sophocles over Shakespeare).
Let me know if I missed anything, and I'll update the post and hopefully we'll have more cheap Bard options coming up.