I would have loved to see a DS9/TNG crossover, during TNG's seventh season. I'm suprised they never did one. It could have been a big two hour epic. There were a few comic book crossover stories.
Well, there were some crossovers technically, although never a large scale one. There was one episode in season six of TNG that took place on DS9 and featured Bashir. Quark appeared on TNG once as well. And of course, several TNG characters appeared on DS9.
I know that's not what you mean though. What do you think would've been the big plot?