I've seen two other sites faced with this problem come up with creative solutions:

http://www.televisionwithoutpity.com - during a time when finances were tight, they sold user-created banner ads. The ads were fun and became sort of a virtual wall on which people tagged jokes and opinions. They were so popular, people were sorry to see the ads go away after TWoP secured steady funding from Yahoo.

http://www.geekculture.com - Geek Culture decided to sell "Super Fan" subscriptions to offset increased bandwidth costs. Super Fans get their own private forum, larger icons, and get to be drawn into a Joy of Tech comic. Perhaps allowing BoingBoing sponsors to comment on posts would work?