Looks like there could be a back-door way to get into Boston, although it probably applies to a very small number of people.
My dad (who got in yesterday) made hotel reservations for Boston back in the summer. He made the reservations through a travel agency that has an official partnership with the BAA. People who already had reservations through the agency may still be allowed into Boston, since the agency is a BAA partner. Here's the text of the email they sent my dad today:
"Dear Runner,
We are sorry to hear that Boston online entry had closed out online before you had time to register. As the official travel agency for the Boston Marathon we are working to secure race entry to the 2011 Boston Marathon for clients who have a name on a pre-existing hotel reservation with us for the 2011 year prior to October 18, 2010 and who are currently qualified to participate in the race.
Please complete the information below and email it back to me. I will submit this information to the Boston Athletic Association on your behalf. Please retain a copy of this email as proof that I have received your initial request. Please, do not contact the BAA directly. They are working hard to work with us and we do not wish to repeat their efforts.
If you have additional questions, please do not hesitate to email me. Please allow two weeks time for additional updates.
Best regards,
xxxxx xxxxx
Marathon Tours & Travel
C-5 Shipway Place
Boston, MA 02129"