Bruce Banner's first appearance in "Hulk vs. Wolverine" pays homage to his last scenes in Hulk (2003), where he is seen at a lake location, and later on being pushed around replies "You're making me angry, you wouldn't like me when I'm angry..." and then his eye colour changes...
A scene in "Hulk Vs Wolverine" features a hall of tubes with floating babies. One of the tubes reads "X-23". X-23 was a clone of Wolverine, the 23rd attempt at cloning Wolverine and the first successful attempt. The character was created by the writers Craig Kyle and Christopher Yost, who worked on X-Men: Evolution (2000) as well as on this feature.
Deadpool is well-known for having the ability of "fourth-wall awareness" in the comics, where he is aware he is in a comic book, and would frequently make comments about it. He displays this ability in the feature, when he tells his teammates to "strike a pose" for the viewer.
Loki exclaims that "The creature's power is incredible!" This is a homage to two titles that the Hulk is known by: the creature, popularized from The Incredible Hulk (1978), and of course the Incredible Hulk line of comics.
Voice actor Tom Kane, who voices Professor Thornton in "Hulk vs. Wolverine," is noted for voicing Professor Utonium in The Powerpuff Girls (1998), Professor Robert Kaufman in Scooby-Doo and the Cyber Chase (2001), and more significantly Professor Xavier in _Marvel: Ultimate Alliance (2006)_(VG).
In the "Hulk vs. Wolverine" story, Wolverine is requested by Departemnt H to hunt down the Hulk. In the comics, Department H is a branch of the Canadian Government that handles superpowered affairs. While Wolverine was an agent of them before joining the X-Men, it is best known for its resident superhero team, Alpha Flight.
The trivia item below may give away important plot points.
At the end of "Hulk vs. Thor" Bruce Banner is seen walking down a highway, while a piano tune faintly plays in the background. This alludes to the famous scene from The Incredible Hulk (1978), where Bruce Banner walks down a road while a piano sonata ("The Lonely Man") played.