Sorry, I neglected to list the DC/Malibu crossover, which is on the DVD. I've amended the list accordingly. Basically the only things it doesn't have (reprints aside) are the Trek/X-Men crossovers, the newspaper strips, and the TokyoPop and IDW stuff that's still in print.
On another site, it was mentioned that the Star Trek/X-Men crossovers would
be included, and the note seemed to come from someone involved in the production of the collection (though I may be mistaken about their role).