Holy cow, I wrote a book!
The principle is that programs you've run most often recently are the ones that show up on the front page of the Start menu. At least, that's what we started with, but it turns out that some fine-tuning was needed in order to get the experience to be more "natural".
The basic rule is that each time you launch a program, it "earns a point", and the longer you don't launch a program, the more points it loses. The Start menu then shows the programs that have the most points. That's about all I'm going to say about the mechanics of point-winning for a variety of reasons.
After the basic rule is applied, the fine-tuning and detail-following kick in. Those are the parts that are puzzling to most people. The next several entries will go into many of the subtleties and fine-tuning behind the Start menu's list of frequently-used programs.
Please hold off your questions until the (two-week!) series is complete, because I suspect a later entry will answer them. (This series is an expansion upon the TechNet column on the same topic. If you've read the TechNet article, then a lot of this series will be review.)
Pre-emptive snarky comment
‡Well, it does accomplish something: It gives me another reason to stop blogging.*
*Along with the people who keep bugging me about using daggers instead of asterisks. Hint: Asterisks already mean something in computer programming.