My favorite "little things" in the movie, more of them are character moments as opposed to easter eggs:
1] Quill's kill of Rao - been mentioned before but absolutely one of those small moments that increased my enjoyment of the movie by a factor. Love how he was hushing her... "It's going to be allright, it's going to be allright"
2] When Pyro and Mags board the convoy with Mystique and they go down the list of the other prisoners --- there's a total easy-going vibe going on between Mystique and the rest [which heightens Mystique's abandonment by Magneto moments later and really adds to the fact that these aren't villains per se]. Anyone else notice this?
3] The half-second shot of Pyro's incredulous face when Magneto says to Mystqiue "You are no longer one of us."
4] A newly depowered (and Brotherhood-dismissed) Raven curling up on the floor of the truck like a potato bug. Absolutely heart-breaking the look on her face. Heart-breaking.
5] Herman Glob's (he looks awesome even if it is for half a second before he gets depowered - can't wait for the DVD to freeze that frame) cameo and the Stepford Cuckoos appearance in the background at Xavier's. Nice to see a shout out to Morrison's New X-Men.
6] The fact that they used a lot of the same background actors for the kids at Xavier's - nice intra-trilogy continuity nod. See Jubilee, the black girl with the afro, Siryn, etc.
7] The way Callisto said "metal" when she addresses Mags "I know you control met'al". Nice to see a little Puerto Rican mutant flavor.
8] The fact that the actress they cast for Jean Grey's mom looks like she could have been Famke's mom. Brilliant bit of small casting there.
9] Eric Dane as Multiple Man. His easy-going "yeah why not?/yeah you got me?" portrayal of the character - (all two scenes of him) was right on.
10] The shot of Raven on the monitor spilling the beans about Magneto's lair. It looked like she was really getting into it, leaning into the desk, gesticulating, you know? Very funny for me. I can totally see her being like "It has twelve bathrooms, eight men's, four women's, but the women's never has any toilet paper..."