I had a small win this morning at work. Apparently, as of yesterday, September 10, 2014, Salesforce made a change such that users with profiles that DO NOT have the “API Enabled” flag checked will not be able to connect to certain Connected Apps. However, the write up on help.salesforce.com doesn’t (at least at the time of this post) explicitly state that Chatter Desktop and Chatter Chat in the browser will be impacted by this change.
So, if all of a sudden today you have users who can’t connect to Chatter Desktop or Chatter Chat in the browser, and they’re getting the “Chatter is not enabled for this organization” error message in Chatter Desktop of the generic message in their browser pop up with a prompt to try connecting again, go into the profile definitions for their profiles and check “API Enabled.” That should allow them to authenticate for Chatter Desktop / Chatter Chat in the browser successfully. Do first consider whether or not their are reasons to prevent the profiles from having API access before doing so.
Josh Gilliam's Blog: Exploring the "PaaSible!" 