In one issue of Excalibur Kitty and Rachel are being accosted by Daleks while queuing at a bureaucratic office
Plus, Merlin's appearance in Cornell's series looks to be a Call-Back to the way he looked in the DWM strip.
Blaze of Glory: In Issue #2, Clay Harder mentions how he buried Matt Hawk and the Two-Gun Kid, and asks Marcel what became of the other Sunset Riders. Both of those are events that occurred in the series of the same name, though its canonicity to this one is debatable.
A subtle one from The Amazing Spider-Man vol. 2 #55: Peter Parker, currently working as a teacher at his old high school, talking to the school secretary (or administrator?) who remembers him from when he was a student:
Peter: Good afternoon, Maude. Looking beautiful as always. Maude: Oh Peter, you lie beautifully darling, have ever since the ninth grade, so don't stop. Ninth grade was when Peter was about 15, i. e. when he became Spider-Man and had to lie to maintain his secret identity.
In a scene in X-Men #3, Professor Xavier privately refers to Jean Grey as "the woman I love." This plot point was quickly dropped until thirteen years later, in #101, when Professor Xavier talks to to Moira McTaggert and bemoans that his telepathic powers "cannot help this girl I once thought I loved as much as you.". After which it was dropped again until almost twenty years later, when Onslaught shows the original scene to Jean in an attempt to prove the hypocrisy of humanity.
Nick Fury and Bruce Banner discuss about his previous time as Hulk, and how he razed the port. The flashback featured Hulk fighting Spider-Man. The scene is a reference to Ultimate Marvel Team-Up #3 and #4.
The recent "mutant hysteria" that Pym mentions in passing was seen in the first arc of Ultimate X-Men (2001).
