Given that a few people in this community have experience with using treadmill desks, this might be a good place to ask other people for treadmill desk knowledge.
If you use a treadmill desk, do you wear shoes while using it?
Do you have data that justifies that choice? Do you have arguments that aren’t data driven that justify it?
Interested to see the debates on this one, as the American Podiatric Medical Association doesn’t recommend one way or another, while sales of minimalist running shoes have grown into a $1.7 billion industry, and this past summer, both Vibram and Adidas were sued in the United States regarding deceptive claims of increased training efficiency, foot strength, and decreased risk of injury resulting from use of their minimalist running shoes.
I for one would prefer a nice cushion. Tim Ferriss also talks about preparing for a marathon in The Four Hour Body:
[quote]Don’t fall for the barefoot myth, either. There is a misguided belief that you can go barefoot
and immediately fix all of your problems. If you have been wearing shoes with heels for years
and start barefoot running with no transition, expect problems with your Achilles tendons. One
year of stretching might get an additional ¼ range of motion out of them, so if you remove a ½″
heel and go pound the pavement, you’re asking for major issues.[/quote]
Personally, I find shoe-less treadmill usage more comfortable, but I don’t have any particular reason for this. (I think it might have to do with the slope of a treadmill deck compared to walking on the ground.)
Scientifically there’s no evidence that going barefoot is any better for your body. That said, most modern shoes cause some deformation of the natural foot shape.
In my experience, after 45 mins of barefoot running using a treadmill I ended up with blisters from the friction. I’m unsure walking would cause the same problem though.
There is some anecdotal evidence that running barefoot or in minimalist shoes hat some benefits:
Hryvniak, D., Dicharry, J., & Wilder, R. (2014). Barefoot running survey: Evidence from the field. Journal of Sport and Health Science, 3(2), 131 - 136. http://www.sciencedirect.com/science/article/pii/S2095254614000337
It is also a nice training tool for improving your arch stability:
Miller, E. E., Whitcome, K. K., Lieberman, D. E., Norton, H. L., & Dyer, R. E. (2014). The effect of minimal shoes on arch structure and intrinsic foot muscle strength. Journal of Sport and Health Science, 3(2), 74-85. http://www.sciencedirect.com/science/article/pii/S2095254614000374
But of course you must ease into it. A shoe is like a crouch. If you leave them you will limp at first.
I’d still wear running shoes. Running shoes are made and improved for our feet’s protection. So even if I run on a treadmill or on the road, I use running shoes. I don’t use barefoot running shoes. If you’re looking for a treadmill, you can visit http://toptentreadmills.com/ and see what is best for you. 
I personally suggest to to it with shoes … I am having my own treadmill at my home place… Life Span TR 1200i Folding Treadmill …Plus point of this is that it offers several weight loss, healthy living, sports training, and heart rate programs
For further details and queries , and information regarding this treadmills are in the link as shown below… It is very much beneficial and it helps a lot to stay active :
Apart from the evidence listed above, in general it makes medical sense to walk / run barefoot for sometime, it helps strengthen the arch of the foot and hence distribute the weight of your body over a broader area as compared to just the center. Hence, helps in preventive back and joint problems in the longer run.
Now, if you suddenly start going barefoot, the fat accumulated over the years on the sole of your foot would still bear most of the load and hence defeat the purpose. Ideal way is to start a few mins a day of barefoot walking, and gradually increase the time before you shift to barefoot running. This will allow the arch of your foot to gain the right curvature over a period of few days / weeks.