Upgrading the CUNY Academic Commons from WPMU 2.7.somethingorother to 2.8.4 went quite smoothly overall. A big problem cropped up a few days after the upgrade, though: integration with bbPress (version 1.0 alpha 6) wasn’t working right. Shared user tables still worked fine, but sessions weren’t carrying over between the platforms – and, worse yet, you had to flush your cookies to be able to log into the other system at all.
A bunch of Googling turned up people with similar problems, but no real solutions (other than the standard setup procedures, such as making sure that the auth_salt etc matched in wp-config.php and bb-config.php). Then I found this thread, where a few people who are smarter than I am had a conversation about WP2.8’s new method for handling cookies. So I understood the problem a little better. Then someone near the end of the thread suggested upgrading bbPress. I did – to bbPress 1.0.2 – and the integration instantly worked perfectly. You don’t even need a plugin on the WP side for it to work anymore.
The moral of the story: The devs at bbPress are awesome. Also, upgrade to bbPress 1.0.2 if you can.