SPOILERS - Not many plot spoilers, but things in general
There’s so many small references, way more than Daredevil, that you’d need to frame-by-frame a DVD of the movie to catch them all, but from memory:
Dr. Hank McCoy being interviewed on TV (Beast)
Reme LeBeu (sp?) listed on the computer along with many other mutants by their real names (Gambit)
Hell, everything on the PC was a link to some mutant or another
Pheonix - the stuff that was going on with Jean Gray
All kinds of mutant kids, from Siren to Jubilee to Kitty Pride to…dunno who the blinking kid was, but he was amusing
As to why the movie was really good. First off, they didn’t pull punches. Wolverine killed with impunity, which was just great. He didn’t back down from murdering anyone. Magneto is just evil - not insane evil, but willing ot murder every human on the Earth because they mean nothing to him. Mystique, on the other hand, could be seen as just someone who truely believes in mutant rights and is going with Magneto for the moment, because she likes his plan best. If there was a better plan, she would probably go with that.
Storm has some serious issues with humans, much more so than in the first. Another hook into her personality that could cause her to change sides. Xavior, on the other hand, is still totally unflappable, even though he was about to kill everyone on the planet.
I like the fact that this movie is not geared for kids. People die, and not because they pulled a gun on the good guy at the last second. There’s obvious differences in the mentality of each main character in the film, it’s not just “good mutant, bad mutant, good human, bad human”. I think because of this, it’s a better movie than the first, because there wasn’t time to show the differences in that one. Finally, people die in really horrible horrible ways - like Magneto’s guard. Sure, he deserved it, but yikes.
The last reason I think this movie was better than the first and in general, really good, is that it seems to be an actual beginning to a full story arc. You don’t know what the president said at the end of the movie and there’s lots of loose ends, so it can go almost seemlessly into the next movie. The first movie ended without any obvious story progression and didn’t leave you with a need to see the next movie to see what they’re going to do next. This one ends with the possibilty of Pheonix coming back, Sentinels being built, Magneto coming up with a new plan, maybe all three.
That’s just my thoughts, after almost no sleep and a midnight showing. Who knows if I’ll change my mind later.