On the iPhone, we design applications around a standard screen size of 320x480. Is there a standard screen size we should use for developing Mac applications, specifically ones targeted to the Mac App Store?
You don't. Desktop computers don't have a fixed size like phones do. Users could have a screen (or two or six) with a resolution anywhere from 800x600 to 3200x2400 or more.
Instead, design your application to be dynamically resizable. Allow the user to resize windows by dragging their corners to make them as large as they want. Ensure that the layout of elements is fluid, and that they move/resize accordingly as their parent window is resized.
Whatever you do, do not try and lock your users into a particular resolution or window size. They will resent it, and your app will not be very successful. You need to abandon the iPhone model when developing Macintosh applications. There are some similarities, but also lots of important differences.
Examine the other applications on your computer, and see how they behave. Good examples are the applications Apple bundles with new Macs, like iTunes, iPhoto, TextEdit, Pages, and Keynote, among others. Certain third-party companies also design award-winning software applications, like Panic's Coda, Fetch, and even Microsoft Office. Hard to go wrong by following their example.