That's an interesting read, regarding Dan Harmon. He seems to have worked out something very similar to the archetypical 'Hero's Journey' underlying most media. I was always a big Community fan, and now that it's pointed out I can really see the structure. That's pretty nifty.
The Hero's Journey is also a great subject to look into if you're examining story structure. It's certainly intense and I wouldn't advise following it step by step, but the general outline has held up for God only knows how long in writing:
If you're talking less about the overarching structure and more about filling 'between plot points' moments with more than just filler, I personally think the best thing you can do is to ask about what you're *changing* with each scene. You can change the characters or their relationships, change the pace, change the tone, change the story direction, etc. It doesn't have to be something big. Even 'fluff' chapters can be great if they're written consciously and purposefully. They can be a break in the tension of the plot, or offer some insight into a character in less stressful or important situations.
((Sidenote: the links to the first chapter at the bottom of your About page and on the table of contents are broken. I dig the site tho!))