Thought this thread could use an updated perspective. Everyone's top five is going to be different, but here are my thoughts having recently gone through the process looking at the academic programs. These are the "top" places in my mind, in alphabetical order. Hopefully others will contribute their perspective.
Emory - Probably the best overall fellowship out there at the moment. Excellent cervical, degen, and deformity experience. Enough trauma, but not a ton. Big names include Heller, Rhee, Yoon and Boden. Fellows were without a doubt the most enthusiastic about their experience of any program in terms of operative autonomy and experience. Unmatched cervical experience with Heller and Rhee. Fellows also have a great lifestyle and good pay with supplemental Grady orthopaedic trauma call. Case load is enormous due to the efficient orthopaedic and spine hospital. Basic science and clinical research opportunities are there, particularly with Boden's lab if interested. Interview was a lot of fun, and you can definitely tell they are very proud of their tradition. Would have loved to have matched here.
Jefferson - Best trauma and degen experience out there. Came to this interview thinking it would be really high, but I felt it took a big hit with Todd Albert leaving for HSS (which was announced the day of our interview...). Fellows still seemed happy and had crazy autonomy. Jeff will remain a great fellowship as long as Vacarro is around, but losing Albert hurt them in my mind. Research opportunities were excellent.
Pitt - Another program that seemed to be near the top of everyone's list. Kang and Donaldson are excellent teachers and mentors. The operative autonomy afforded to the fellows was outstanding, but the faculty were still around to teach. Fellows were very happy and enthusiastic about their experience. Research factor was ok, not the best, but made up by the camaraderie between staff and fellows and operative experience. Great exposure to bread and butter degen spine, peds deformity, trauma. Not much in the way of adult deformity, which could be a good thing depending on your perspective (for me a positive). Pittsburgh was affordable, but boring if you are single. Really liked this program.
Rush - Rush has been and continues to be among the top programs in the country, it has just changed its flavor in recent years. The unique thing about the Rush fellowship is the minimally invasive experience. Frank Phillips seems to be the emerging big name here and between him and Kern Singh, the minimally invasive experience is unparalleled by the other top programs. Howard An seems to be slowing down. This and living in Chicago for a year were very appealing to me. Fellows seemed genuinely happy with the experience. Zero trauma exposure.
Wash U - Didn't interview here (conflicted with Pitt), but from all accounts this remains the place for adult deformity. They put out a ton of research and the cases are very complex. People I talked to on the trail were somewhat turned off by the effect of the "super fellow" and the high floor work load.
Honorable mention :
Leatherman - Very surprised by this interview. Great operative experience and autonomy. Big cases, including lots of deformity. Downside was possibly limited cervical experience (learn from neurosurgeons for the most part), fair amount of service-work (PGY-6 feel), and primary level-1 thoracolumbar trauma call Q4-5 (i.e. the ER has your pager # and all cervical trauma goes to neurosurgery), and no MIS. Research opportunities were much better than I had thought.
Stanford - Didn't interview here, but people I knew that did loved it.
NYU - Excellent deformity exposure, reasonable MIS, great research machine, wasn't sure about the fellow autonomy factor. No trauma exposure.
OrthoCarolina - Had to cancel this interview due to inclement weather, but heard a lot of people really liked it here. Great clinical experience with good lifestyle and pay (supplemented call). Limited trauma and deformity. Not a research powerhouse. Darden is a stand-up guy by all accounts.
Utah - Great all around exposure, good autonomy. Excellent degen, deformity, and trauma. No real MIS experience. Brodke is the man and would be a great mentor down the road.