The Ultimate Edition has 2 other commentary tracks with the cast, a DTS track, plus a fullscreen version of the movie on the second disc. The "Ultimate Edition" was made and distributed by Columbia Tristar, whereas the "Collector's Edition" was by Universal.
As far as the R1 editions, while the Ultimate Edition added a host of new features over the initial Collector's Edition, one major thing it dropped was the isolated score by Jerry Goldsmith.
I for one enjoyed "The Mummy", but the only differences between it and it being an "Indiana Jones" adventure is the absence of Harrison Ford and an extra $100 million box office intake.