It's only 1/3 of the whole shebang, but it's still important to have a good, trusty pair of shoes on your feet for the running portion of the triathlon. Pick up a pair of running shoes that are expertly tailored for your feet. Take a trek down to the local specialty running store, get your stride and foot measured, and let the experts there pick out a shoe that will provide you with the maximum amount of support and comfort.
This is one area where you might not want to go cheap. If there's anything in the world to drop a few bucks on, it's your feet; they'd thank you for it (if they could talk).