I have had neck pain but I have chronic migraines as well as jaw problems that can cause neck pain and a tendency to sleep in strange positions...so it wouldn't be fair to associate the neck pain with the sensation without ruling out my other conditions first.
I don't know what it could be, but you might want to mention it to your doctor to see if they have anything to say about it. I've also been having a lot of popping in my head and I can't seem to find any good information about what it could be. I do see that a lot of people have said they experience it.
Have you had any neck pain or problems with your cervical spine?