Admittedly, I could have easily missed other homages because I haven't read or seen the entirety of the Superman canon. So if you have caught other homages, please leave them in the YouTube comments. Mine draw on the movies and the comic books that I've appreciated over the years, but I also think these are ones that were close to the filmmakers' minds (e.g., David Goyer wrote the forward to Superman: Secret Origin and talked about how certain scenes by Geoff Johns really made him connect with Superman in new ways).
If you're curious about what prior material had the biggest influence on Man of Steel, here's my tally (though they aren't necessarily all of equal importance):
- Superman: The Movie (Donner) - 8
- Superman II (Lester) - 5
- Superman: Earth One (Straczynski) - 5
- Superman: Birthright (Waid) - 4
- Superman: Secret Origin (Johns) - 2
- Superman: Last Son of Krypton (Johns) - 1
- All-Star Superman (Morrison) - 1
- Action Comics #1 (Siegel) - 1
- Superman #1 (Siegel) - 1
- Superman: The Animated Series (Timm) - 1
- Superman Lives (Peters) - 1
Credit goes to Man of Steel Answers (MOSAIC) for catching the Action Comics #1 tribute.