1. Categories. This is the most obvious thing, and yet you'd be amazed how many cafés mess it up. Start with the biggest, most popular category on top. Usually that's "Coffee" or "Espresso." Then move to "Tea." Then move to "Other Drinks." Then "Food." Then "To-Go Items." That's it.
What you don't do is hide the coffee in the middle. I saw a café once that had "Food" first, "Tea" second, and "Coffee" third. The line was slow. People were asking, "Where are the lattes?" It was a disaster. Put the money-maker first. Always.