Putting aside any crossover on which I worked, and so cannot be objective about, there really hasn’t been anything to match that first SUPERMAN VS THE AMAZING SPIDER-MAN book. I’m sure it’s difficult to understand what a bombshell that project was when it was announced in 1976–like a joint U.S./Soviet space mission or something. And it’s a good book, adroitly combining the styles and flavors of the SUPERMAN and SPIDER-MAN series of that period into a single story.
Now, probably the best from a qualitative standpoint was the X-MEN/NEW TEEN TITANS book. It’s a rock-solid piece of work.
Of the later crossovers, there were a bunch I liked: PUNISHER/BATMAN: DEADLY KNIGHTS, DARKSEID VS GALACTUS: THE HUNGER, but somehow these later ones aren’t quite so special to me–likely because I was working at Marvel when they came out, rather than just being a reader.
In terms of a crossover that hasn’t been done before, Walt Simonson had a great pitch for a THOR/NEW GODS story that he was interested in doing back when he was working on ORION, but it never happened–so maybe that. The other obvious one in a modern context would be BATMAN/IRON MAN.