I ran into a little problem on my development server today. I was playing round with a windows service that I wrote to run timed events. At one point the Windows service ran into an infinite loop and "End Task" wouldn't kill it, so the only way I could break out of it was to restart ISS. All of a sudden the windows service would no longer start. After a while I tried to log into the crm incarnation of the organization I'm working on and I kept on getting a "The specified organization is disabled" error. This made me panick a bit because I thought I'd corrupted the DB. After more time trying to figure it out, I also tried each of the other organizations (there are 10+ of these) on the crm server and they all had the same problem, "The specified organization is disabled".
Googling the problem kept on coming back to an issue with disabling the default organization form within Deployment Manager. But since I had not done this, I just ignored it's advice and kept on trying to find BD corruption. But after a while I had a look at Deployment manager, and sure enough, the default organization was disabled. This puzzled me a bit, until I remembered that I did infact disable it weeks ago. So I had a look at this link:
It was clear that, by pure bad luck, I had not restarted IIS since the default organization got disabled, which was weeks ago. So, re-enabled the default organization, restarted IIS and everything was working again. But 4 hours was wasted on this problem.
Moral of the story, the most obvious cause/solution is often the most likely.