It's been some time since I've watched it all the way through, but as I recall there's a couple of additional scenes. The most notable addition is that the Ultimate Cut has the Black Freighter cartoon edited into the movie (along with additional scenes of the kid and newstand owner.) Anyone who's read the comics will tell that's a pretty integral part of the story insofar as the subtext of the overall narrative is concerned.
Both the cartoon and the Under the Hood faux-documentary (which isn't edited into the film if I remember rightly) are also available on their own as bonus content. I think it also has a weird kind of "full motion comic" version of the graphic novel, as well.
Honestly? I thought it was pretty cool to see it all cut together like that. However, as "a movie," it didn't feel as cohesive. It just overall feels too dissimilar from the rest of the movie, visually - and you can also kind of tell that the live-action portions from the Black Freighter were shot by the "B" crew.
I'd say it's worth spending the money for the Ultimate edition, just for the bonus features, though.
Personally, I really enjoyed the movie as a companion to the graphic novel. Your enjoyment is really going to depend on what you expect to get out of a film adaption of a comic book like this. Obviously, it's not as "good" as the comic (which I rate as a high point of literature, not to mention solely the realm of sequential art,) but I still think it was pretty darned cool. The opening sequence alone I really enjoyed.
