Latest Editor's Note got me thinking about it and I wanted to try to put together a list of the art references that I recognized (I have to look up some issue numbers, but the ones I'm listing are the ones I know what to look for).
Argent Adept incap: Uncanny X-Men #251
Freedom Six Bunker incap: Iron Man #128
Fanatic incap: X-Factor #10
Haka incap situation is evocative of the cover from Secret Wars #4, but the pose is more like this panel from Incredible Hulk #358
Idealist incap: House of M #1 (variant cover)
K.N.Y.F.E. incap: X-Men (vol. 2) #25
Legacy incap: Superman (vol. 2) #75
Young Legacy incap: Crisis on Infinite Earths #7
Greatest Legacy incap: Captain Americal (vol. 5) #25
Dark Watch Mr. Fixer incap: Daredevil #181
Setback incap: Amazing Spider-Man #50
Dark Visionary: X-Men #137
Wraith incap: it's entirely likely that there's a specific one that I'm unfamiliar with that's a better match as "superhero graves" are a common enough trope, but there's Daredevil #182 and #509 or Web of Spider-Man #32 for some examples.
Freedom Six Wraith incap: there are a bunch of "bad guy holds hero overhead" options to go with (see also Naturalist's incap) but the best match I think is this one from Batman #497
Fright Train incap: Uncanny X-Men #322
Visionary's Mind Spike: X-Men (vol. 2) #25 again
Guise's X-TREEEEEEEEME!!!: Basically any Rob Liefeld-drawn cover featuring Cable, here's X-Force #1
K.N.Y.F.E.'s For the Greater Good: Also that panel from Daredevil #181
K.N.Y.F.E.'s Kinetic Neutralizer: X-Men (vol. 2) #5
Chokepoint's Harvest the Mighty: X-Men Omega (the finale of the Age of Apocalypse story)
Anyway, that's what I've come up with. Anybody else have any others they're familiar with or better matches for any of my examples? There are a bunch of pieces from SotM that seem like they're specific enough to be refering to specific images (like Proletariat's incap seems like it should be a Winter Soldier reference or something but not something that comes immediately to mind like most of these).