The Three-Act Structure and game jam games
Here's some thoughts I had while writing the story for my entry. I'm no expert on this topic so take it for what it's worth. And please correct me or elaborate if you know better!
The three-act structure is a classic storytelling technique most common in motion pictures. I think it also works great for games with a narrative that are, roughly speaking, less than 4 hours long. (Although some Zelda games manage it while being much longer.)
I certainly don't think that PyWeek games need a narrative, but if you want to include one, this structure matches up well with how the player typically encounters mechanics. Essentially, Act 1 is the tutorial or the introduction of the major mechanics, Act 2 is the main gameplay where you introduce variations on the mechanics or more involved challenges, and Act 3 is the final dungeon, boss, challenge, etc. Act 2 can be open and have separate branches, but typically you bring everything together for Act 3. richard's PyWeek 12 entry came with an excellent plot diagram that shows this off visually.
In terms of the narrative, there's a plot shift, also known as a plot point or a reversal, between Act 1 and Act 2, and another between Act 2 and Act 3. These can be twists, where some secret is revealed (e.g. the Act 1 reversal in The Matrix is a twist), but they don't have to be. Within each of the three acts, the protagonists have a different immediate goal. The Act 1 goal can be low stakes, vague, abstract, or mysterious, but Act 2's goal should be clearer, and Act 3's goal should be very clear and concrete (e.g. escape or defeat the boss). Often the act change coincides with a change in location (e.g. every Star Wars movie).
You'll often see it said that Act 1 needs an early inciting incident or call to adventure (e.g. The Wizard of Oz, Jurassic Park), and that's a good idea but IMHO it's okay to just use Act 1 to introduce the status quo of the world and characters, and let the plot events really start with the shift at the end of Act 1 (e.g. The Lion King, Shaun of the Dead, Back to the Future).
Some more general guidelines. Act 2 is the longest, about twice as long as each of the other acts. In my experience this means moving as much exposition as possible out of Act 1 into Act 2. Introduce characters early, ideally in Act 1, even if they're not important to the plot until later. Acts 1 and 2 can take place over days or years, but Act 3 generally happens in a single day, or even in real time.
Again, that's only one way to do things, but I've found it useful, especially this time.