This post is a result of my rereading Madden's 99 Ways to Tell a Story for my recent review. The list could obviously be extended far beyond the symmetry-pleasing 9 -- that's part of why it's such a good book.
1. The final panel in the "Upstairs" variation, in which Jessica's moody silence and staring-off-into-space posture services to replace the "What the hell was I looking for anyway?" thought balloon from the template.
2. The way that the normal speech balloons -- and thought balloon! -- from the template are half-visible through the window, behind the grated bars, in the "Voyeur" variation. (Compare the outside view in panel five of the "Extreme Zoom" variation where the word balloon is outside the bars -- each appropriate to their context, of course.)
3. The upside-down speech balloon in panel four of the "Underground Comix" variation.
4. All the details in the final panel of the "High Noon" variation-- the hidden gunmen out to get him, and the dangling watch unveiling the plot of the whole page: that the sheriff mistakenly thought it was high noon, but that it was actually 1:15 (hence the upstairs woman's "hee hee") and therefore was trapped.
5. The shoe on the oven in the "Opposites" variation -- reversing the hat on the refrigerator.
6. Madden's flowing hair in the "inking outside the box" variation.
7. The fact that the hat on the refrigerator in the "Linge Claire" variation is Captain Haddock's cap. (Also the computer becoming a typewriter.)
8. The thematically apt pauses in the "Calligram" variation: "You interrupt me en//route wanting to know how//long you have been//procrastinating", with the shape recapitulating the events.
9. The saga of the one-eyed space-alien magnet. This is most clearly visible in the "Things are Queer (after Duane Michals)" variation, where you actually (for good structural reasons) get a good look at it in panel two (which is why I first noticed it). But yes, it's actually visible on the fridge in panel four of the template, as well as in many others -- though the only way to be sure it's the same is to look at the "Maximalist" variation, where it is visible not only in panel four but in panel six as well -- recognizably the same thing as from the "Things are Queer" variation. Interestingly, although the setting for panel four of the "Plan 99 From Outer Space" variation is largely unchanged, it looks to me like the magnet is drawn just a bit more clearly in that one (or am I imagining it?). Finally, the magnet (along with the others) are moved in "What's Wrong With This Comic", for one of the promised two changes in panel four.