PhakeDoc, this is a great question. I battled with idea of ranking last vs not ranking at all for quite some time. In the end I decided to leave 2 programs unranked for personal reasons.
1) Vanderbilt - They have a terrific program with great faculty. However, I really didn't get the feeling that I fit in on my interview day. I don't want to take anything away from the reputation of the program, but it was merely a personal decision not to rank them. Although Nashville is a great city, I just couldn't envision myself living there for the next 4 years and being happy.
2) Harbor UCLA - They seem to have a solid reputation for churning out good neurologists. However, the facilities and shear number of faculty (5) deterred me from ranking them. There is just too much instability with such few faculty.
While both programs are great programs, I just didn't feel like they were right for me. I already had 10+ program I ranked, so I didn't feel it was necessary to add them as backup programs. I would be curious to see what programs other people left unranked.