As stated earlier, USNA can only grant waivers for admission to USNA itself. In other words, just because you get a waiver from USNA, does not mean that you will get one from West Point, or even NROTC for that matter. Additionally, as A6E pointed out, a waiver for admission is not the same as a waiver for comissioning.
Colorblindness was one of the main ones I was thinking of. You can only serve in a restricted line community (think Intel, Supply, etc.) in the Navy or go Marine Ground (with some limitations on MOS I believe).
Eczema is another. I had eczema that was very mild and well contained (I've posted about it before, you can search for it), and was waived to commission into any field. I had a friend that had eczema but continued to have flare ups which required medicine while they were at the Academy, and they were only able to go SWO. A third person with eczema was deemed non-commissionable and got the golden handshake.
I've also heard of some people who had major surgeries as children (like knee etc.) who were waived for admission but had some trouble come commissioning time. Some were cleared to do what they wanted, others were forced to go SWO or restricted line. Their circumstances were varied and unique and I can't speak to why those individuals got the outcomes that they did.
I will say that I might have been a bit trigger happy with my first post. The fact of the matter is that the number of people that aren't able to commission due to something that did not develop/get worse at the Academy is extremely low and not something I would spend time worrying about.