All of the long-term projects had an artist assigned full- or part-time to the authoring team. Artists would build the look of the interface in the art application they were most comfortable with (almost universally Adobe Photoshop).
This had an interesting effect: Artists tended to design functional aspects of the program that, had they been building something more prosaic like a spreadsheet, they might not have designed. For example, in Immunology, the artist made beautiful colored scrollbars with backgrounds and thumb tabs that matched the color scheme of the application, and was unhappy to discover that the Apple Toolbox interface provided much less control than she wanted. Another example is having artists draw impressive-looking load and save dialogs, even though the Mac provides functional ones by default.