I have tried all the recommendations on the web, to no avail.
I wrote a console application per these instructions: http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.spcontenttypecollection.delete.aspx
The "Usages.Count" is = 0. Yet, when it tries to delete the Content Type I get an Exception:
"The content type is in use."
This is a brand new (development) install. I created a test site in SP Designer, created a Content Type,then a list. Then, I removed the list, removed it from Recycle Bin and tried to remove the content type...... Ugh.
I was frustrated by this issue until I found your comment. Excellent advice.
That's a lot of recycling! Once complete, I was able to delete the content type.