Perhaps a bit optimistic to try to collect all trail-related (and no doubt some that are not) foot ailments in one thread, but I'm game ...
(1) Bunionettes, i.e., little-toe side bunions, often with accompanying under/overlapping little and next-to-little toes which can sometimes blister as a result. Solutions: surgery, or get shoes with a wider toe box, plus on occasion injinji (toe) socks for the toe lapping thing. I passed on the surgery; Golite shoes for me, always interested if a supposedly "wide toe box" shoe of another brand resolves this particular problem for others. Hint: I walked almost 50 miles on one trip with shoes that didn't work before the gradually increasing ache made it's way into my brain that "these shoes don't work". So it's not something I can figure out in five minutes in a shoe store.
(2) Morton's Neuroma. Something more common in women who wear high heels, nerve damage in the area of the ball of the foot. I just did have surgery for this. Dunno if the tread pattern on my Golite shoes was a factor in getting it or not, but there was an obvious "click" as things shifted inside my foot in that area, and a low grade discomfort bordering on pain that was just never going to go away without the surgery. I recall reading somewhere that someone was using kevlar stiffener in their shoe for something along this line, not an insert, just something that presumeably goes below the insert. In looking for something like this later, I've not run into anything, so if anyone has any leads (and/or experience) ...
(3) Something mysterious in the arch of my right foot. Like the Neuroma this started happening in the last few hundred miles of my PCT thru-hike in 2008. It just feels sore, kind of achy. My foot doctor couldn't make it hurt through manipulation, it only bothers me after I've been standing/walking on it for a while. He theorized some sort of soft tissue problem that could be cured through immobilization, but after a month in a walking cast the problem is still with me, thus I don't think it's anything like a stress fracture. Occasionally it feels like it shoots up my ankle towards the ball of the ankle a bit. I'd really like to at least diagnose this one.
Feet are complicated. I can't wait to find out what new problems are in store for me on the Appalachian Trail this year! :-)