If you're getting the following exception when trying to delete a content type ("Microsoft.SharePoint.SPException: The content type is in use"), here's a quick checklist of things to check:
1) SPContentTypeUsages. Using SharePoint Manager, you should be able to see whether your content type is used on any lists or libraries, and you haven't removed them yet.
2) Make sure you remove all items from the User recycle bin:
3) Make sure you remove all items from the Site Collection recycle bin (this is the step that I always used to miss out; sometimes also known as the second stage recycle bin):
Only when you've tried all three and you're still getting the error can you then start thinking about possible corruption in the content database, but I really wish I'd thought of checking the second stage recycle bin a lot sooner...