I think a crossover is a true crossover if one of two things happen.
1) The crossover has a substantial effect on both universes, and that effect is taken into account in the writing of future adventures for both universes.
2) Like the X-Files/Homicide/Law&Order crossover, nothing drastic happens to effect either universe and they go their separate ways. The crossover still happened, and therefore they exist in the same universe, but it did not create any fundamental changes to any of the participating series/characters/whatever.
My favorite crossover: In the second episode of "Chuck," he flashes and starts talking about where Oceanic Flight 815 went down. So clearly "Chuck" and "Lost" are in the same universe, but it doesn't matter at all because the stories are so unrelated.