Reference to the Two Papers cited in these discussions:
Lawrence M. Witmer "Nostril Position in Dinosaurs and Other vertebrates and its Significance for Nasal Function
August 3, 2001   Vol. 293   SCIENCE
Paleoneurological evidence against a proboscis in the sauropod dinosaur Diplodocus by Fabien Knoll, Peter M Galton, and Raquel Lopez-Antonanzas
Geobios   available online Jan. 20, 2006
Sauropod's Trunk First Notes     Review Notes      Diplodocus Notes     Models of Brachiosaurus
The Brachiosaurus Discussion
Quoting in part from "Paleoneurological evidence against a proboscis in the sauropod dinosaur Diplodocus" by Fabien Knoll, Peter M Galton, and Raquel Lopez-Antonanzas, they noted in their conclusion, ". . . .but not for Brachiosaurus (although the presence of a proboscis in the latter genus has not been convincingly argued, this hypothesis remains)"
I take this to mean that while they feel the Brachiosaurus trunk idea hasn't been argued well, it remains as a valid hypothesis to consider and study. I concur that it is a valid hypothesis deserving further study.
The paper by Lawrence M. Witmer, titled "Nostril Position in Dinosaurs and other Vertebrates and its significance for Nasal Function"  addresses the generalization across all dinosaurs where the nostril opening on the skull appears far larger than an expected nostril opening in the skin would be, and he illustrates the concept on a Brachiosaurus, a T Rex, and a Triceratops.
His generalized conclusion, that nostril openings in the skin should be in the lower and more forward position of any set of position options tends to agree with my notes which stated: "As such, it (the nostril openings of the skin) should be situated close to the mouth. It should be situated at the front of the face so the head can point the nose at a source of odor, and ideally, the eyes should be able to see what the nose is smelling so that the brain can get a visual/olfactory correlation." So it seems that Mr. Witmer's paper and my notes do concur on that matter.
He does illustrate a Brachiosaurus head, and he puts the nostril openings of the skin at the lowest and most forward position of the nasal shelf of the skull. I altered my two Brachiosaurus Sculpture photos into a composite resembling Witmer's concept, as seen below.
Low and Lower
I suggest the nasal openings may be even further forward and lower, as on the end of a short trunk, so in that I disagree with Mr. Witmer. But nothing in his notes that I could find specifically excludes the trunk hypothesis as an option. And a trunk of some kind does in fact satisfy his basic concept, that the nasal openings should be low and forward relative to the skull's nostril openings. The trunk is simply an extreme variation of his argued positional preference (lower and more forward skin openings as compared to skull opening). So while Witmer doesn't offer any argument in the paper specifically disproving a prehensile trunk-like appendage on Brachiosaurus, I would think the hypothesis remains open to discussion.
But clearly, even one glance at the skulls of Brachiosaurus and Diplodocus leads us to conclude there are two profoundly different evolutionary influences, resulting in two profoundly different skulls. Where the Diplodocus has a rather typical skull similar to many existent species (except for the nares at the top of the skull), the Brachiosaurus has a skull like nothing we've ever seen. It simply is unique.
The massive shelf above the upper teeth, the huge nasal cavity, and the curious delicate arching bone rising up like the St. Louis City Arch, all add up to a very different mystery than Diplodocus. I have visualized a hypothetical skull for Brachiosaurus, if we had Witmer's facial visualization as our only reference, and we were trying to "look beneath the skin" and imagine the skull that would likely correspond with his suggested position of the nostrils exiting through the skin. It makes perfect sense, except that we know the real skull is utterly and profoundly different.
The reason I personally do not endorse Witmer's intrepretation, as illustrated in his paper and above here, is that he sees the massive concavity in the Brachiosaurus skull, and places his proposed nostril openings in the skin low and far forward at the tip of this huge shelf, yet he seems unconcerned with any explanation of why this bizarre shelf exists. To me, addressing the nostrils while not addressing the huge concavity behind the proposed nostrils is like re-painting a car that's been totaled in an accident. The priority seems misplaced.
Yet in another regard, the Brachiosaurus has a much more mundane (if incredibly massive) body shape, with remarkable similarities in convergent evolution to the modern giraffe. It simply has a logical and easily understood specialized high browser body (as compared to the Diplodocus body which is an engineering mystery)
The giraffe has a prehensile appendage to assist it in food gathering, an that is its tongue. So arguing that a specialized high browser would benefit from some prehensile appendage to assist in food gathering is supported in that generalized comparison. Why nature would choose to make the lip instead of the tongue as the chosen prehensile appendage is something we can only speculate upon, but just looking at rhinos, and the curious difference between a white rhino (with its broad, flat grazing lip) and the black rhino (with it's pointed and somewhat prehensile lip) certainly shows us that prehensile lips can occur.
So I personally think that suggesting the Brachiosaurus had some type of prehensile appendage to assist in its food gathering as a specialized high browser is a reasonable suggestion to explore further. And the massive concavity in the upper jaw/skull suggests to me that's where the suggested prehensile appendage should be located, which makes it a lip/trunk structure instead of a tongue structure. After all, it's my understanding of anatomy that any conspicuous concavity or indentation of the skull usually houses some type of muscle array or an organ.
Other Thoughts
And what about that curious arching delicate bone along the centerline of the skull? Well, I'm willing to take a guess here, a hypothesis of what it might be for. It seems to me delicate bones are for attaching delicate muscles and organs, and the base of any trunk could hardly be called delicate. My personal inclination is to look for some type of larynx-like vocalizing muscles that might attach to that arch and provide a richly complex vocalizing capability for the air being expelled through that passage outward.
Some people who commented about the suaropod's trunk, in the two Cryptomundo articles written by Loren Coleman, seemed to feel the sauropod trunk issue was emphatically settled as no longer a valid hypothesis. After reading both Witmer's paper and the one by Fabien Knoll, Peter M Galton, and Raquel Lopez-Antonanzas, I personally have not seem any argument to convince me that we should not continue to explore the idea and consider a prehensile trunk of some form on the Brachiosaurus, similar to the one I sculpted and show in this gallery.