A common problem in SharePoint 2007 is when you need to delete a Content Type from a List or from a Document Library: you receive the error 'The Content type is in use'. Ok, you understand that there is still a List or a Document Library that is using it and even if you remove all the associations from all your lists if you try to delete it you could receive again the same error.... 'The Content type is in use'
What's going on?
If you look at the msdn you will read that:

A content type cannot be deleted from a list if that list contains items of that content type.

So the problem is that you still have items in your List that are associated to that Content Type. A fast workaround is to select all the items, send them to the site's recycle bin, remove the Content Type and finally restore all those items from the bin back to the List.

msdn reference: http://msdn.microsoft.com/en-us/library/bb802962.aspx