During the Harry Potter parody, Deadpool points a gun at Batgirl asking what she did to the real one. That's because he's a Marvel character and aware of the Kree/Skrull War.
Superman attempts to get Ben Grimm to mock Dawn of Justice by pointing out how it's too dark and has a lack of humor. Unfortunately, these were criticisms of the new film as well, so it didn't help at all.
Iron Man threatens Spider-Man if they "put a teen vampire into your reboot." While they never did, Morbius is one of Spider-Man's rogues, and in some continuities, he is in fact a teen vampire.
In the Rorscach & Deadpool Buddy Cop parody, the pair are on the trail of a mysterious crime figure named Joe Palachi, who turns out to be The Joker, and more specifically the humorless 80's one from Frank Miller's Batman: The Dark Knight Returns. There are about three layers of brilliance to this, one of which Joe himself admitted to being the reason he picked it:
Firstly, Palachi, whilst being a sort-of common Italian surname, is also a reference to the opera Pagliacci, and the lead character of the same name (it is sometimes called Palachi's Opera). That was a subtle clue as to Joe Palachi's true identity.
Secondly, this is a Watchmen reference and specifically a Rorschach reference, since in the comic Rorschach tells someone about a joke he heard about Pagliacci.
And third, the joke is about how the great clown Pagliacci is utterly depressed and miserable because he has come to view the planet as a Crapsack World, which perfectly reflects the fact that The Joker pretending to be Joe Palachi is the most serious, unfunny Joker ever put to print- turned up to eleven when it turns out Darkseid has brainwashed him with the Anti-Life Equation which makes him really believe this:
"Man goes to doctor. Says he's depressed. Says life is harsh and cruel. Says he feels all alone in a threatening world. Doctor says, "Treatment is simple. The great clown Pagliacci is in town tonight. Go see him. That should pick you up." Man bursts into tears. Says, "But doctor... I am Pagliacci.""
Another example is just in the pairing of those two Deadpool is a walking Satire/Parody of comic books antiheroes/anti-villains , whilst Rorschach is a Deconstruction of the Anti-Hero/Anti-villains.
In the Meanwhile series, the Spider-Man from the 60s mentions that Venom momentarily triggered his Spider-Sense before he was calmed down by the other heroes. Some viewers may initially see this as a Series Continuity Error, since one of Venom's best known and intimidating features is how he is immune to the Spider-Sense. However, it actually makes sense. Venom is immune because his symbiote was originally bonded to Spider-Man, but the 60s version of Spider-Man has not worn the symbiote yet, so his Spider-Sense would be able to detect Venom and any hostile intent he had.
