I thought Amalgam had way more of these...

Spider-Boy gets to his third reboot of the the Legion of Galactic Guardians 2099 in Spider-Boy Team-Up #1, "Too Many Heroes--Too Little Time!" Written by "R. K. Sternsel" (Karl Kesel and Roger Stern) with art by Jose Ladronn and inks by Juan Vlasco.

I think he might have a bit more Superboy than Spider-Man in the mix, but Spider-Boy was one of the more entertaining Amalgam books, and would get an issue in both runs. I'm hard pressed to say if any other books reference the "Secret Crisis of the Infinity Hour," although DC and Marvel did a pretty good job not overlapping characters in that event. There are at least a couple more fake crossovers scattered throughout Amalgam, though; I reckon we'll see another one later.