Does the toe iteself look crooked or misshapen? Is it longer then the others? DOes it normally sit on top of either toe next to it, or get crammed into your shoe in a funny way? Does your toe bend under, keeping it from sitting flat on the ground?
I don't know what it is that's wrong with it, but they make cushions and such for problems like that. If you don't find something at your local pharmacy, footsmart.com has a great selection. COULD be hammertoe, but I would think your doc would have thought of that.
You know I have lots of foot problems. I have had good luck with the brand Profoot Care
Also, I can't push those Yoga Toes enough!
Also, you may have broken it at some point, and really, there's nothing you can do about a broken toe except for your big toes. I actually broke my big toe back in college (dropped a crate of records on it) and never got it set - it still gives me problems to this day.