He has an idea for an elemental sorcerer who happened to be born blind. Wishing to give their child sight, they traveled to the land of Alkenstar and managed to have the engineers of the duchy extract his useless eyes and replace them clockwork ones. These new, technological eyes would grant him the darkvision ability that dwarves and half-orcs possess.
Now, I like it when my players come up with interesting concepts and I always try my hardest to help them represent some of those concepts within the rules of the system that we happen to be using at the time. I also believe in making deals with players who want something for their characters because nothing comes for free.
Using the above example, the players wants their character to have artificial body parts that grant them an ability that humans usually don't have within the d20 system. However, I don't want to give it too him for free. So, if he decides to use this character, I'd probably have him trade the bonus feat that humans usually receive and replace it with the darkvision ability.
I really believe more Game Masters should be willing to make these deals with their players. All you have to remember is to make the player agree to a condition or make a payment in return for the ability.
For example, let's say your player wants to begin the game with a masterwork rapier that his father once forged for a customer with an extra finger on one of his hands. However, the father refused to give the blade to the customer and was killed by him for it. This blade is all the character has left of him and hopes to use it to kill the customer and gain vengeance for his father. A very original concept indeed.
Being the GM of this hypothetical player, I would most likely allow him to have this masterwork rapier with one, simple condition: they can never sell or get rid of it. Since this is the only thing the character has of his father's left and it symbolizes his current purpose in life, I think that's a pretty fair condition.
However, there should be a limit to this. You shouldn't make a deal if the only reason the character wants something for purely mechanical reasons. Also, you shouldn't make the deal if the thing the character wants would make them really overpowered or the equivalent payment would most likely make the character unplayable. For example, making a deal for a player who wants to be able to use finger of death as a spell like ability at will might be a little much.
Just remember to keep the deals in check and make sure the payments and conditions are equivalent to what the player wants. If you keep those in mind, making these kinds of deals shouldn't be problematic.