Bishop has an I.V. running from his arm to his rifle, allowing it to charge with and fire the energy he absorbs from Sunspot.
The magazine cover with Bolivar Trask ("Rolling Stone," I think?) has an insert headline in the upper right-hand corner, "The Spy Plane We Don't Talk About"...alluding to the fact that the X-Jet of the original comics was based on the still then-classified SR-71 Blackbird.
Stryker's dogtag says he's Protestant, surely a reference to his origin from the comics in "God Loves, Man Kills."
Xavier drinks Tanqueray gin and Johnny Walker scotch and Jameson whiskey. Couldn't recognize the other bottles. CHEERS!
Xavier says, "TOP MARKS, you are perceptive," betraying his history as a (retired) professor.
His files show Azazel and Angel's corpses...who was the first corpse seen before theirs? Magneto later mentions both Emma Frost and Banshee were killed and studied as well.
As the group infiltrates the Pentagon to free Magneto, they break away from a tour guide, echoing the similar scene opening X2: X-Men United with Nightcrawler infiltrating the White House.
Wolverine is standing in front of a fine art painting of soldiers from French history, one of which bears a STRIKING resemblance to HIM. AWESOMENESS.