Looks like the only difference is that one comes with an additional BD3D and the other does not. They are exactly the same price though which is a tad unusual.

Edit: Nevermind. 3D set comes with this plus the stuff in my next post. (It was too long for one post.) But both sets are $25 so it's a no brainer, obviously.


Exclusive Bonus Features Disc

The Furious Gods: Making Prometheus (1080p, 3:40:56): Here's where it really gets good. Directed by renowned behind-the-scenes documentarian Charles de Lauzirika, this nearly four-hour making-of feature is a comprehensive journey through the film's creation—from early script ideas to the pre-release hype train—with all-access on-set footage and interviews with nearly everyone involved. Read below to see what's covered in each of the nine sections.
Conquest of Paradise: Renewing the Story: Ridley Scott and the film's writers discuss the process of revamping the series, drafting up the initial scripts and moving into pre-production design.
Under the Pyramid: LV-223: Here, we go inside the art room in Los Angeles where the film's visual ideas were hashed out, see a meeting with H.R. Giger, hear about the designing of the "space jockey's" chair, and even hear how the artists were initially opposed to the humanoid look of the Engineers. We also get into the evolution of the monster design, which will be fleshed out in it's own section later in the documentary.
Reverse Engineering: USCSS Prometheus: A look at the designing of the Prometheus ship—from the functional aspects of spaceflight to the technology of the interiors—along with the rovers and ATVs.
The Human Manifest: Casting and Costumes: An overview of—and interviews with—all of the main actors, discussing their characters and how they got involved with the film. Best bit? An outtake with Michael Fassbender, as David, referring to his android penis as "sixteen inches long when erect; it varies when relaxed." Mixed in are interviews and behind-the-scenes footage with costume designer Janty Yates, explaining the rationale behind the characters' outfits.
A World without Green: Pinewood Studios, 2011: Ridley's decision to create as much practically as possible—as opposed to automatically defaulting to greenscreen and CGI—resulted in some huge and remarkably detailed sets at England's Pinewood Studios, specifically the famed 007 lot. We also get a look at the process of shooting in 3D, from the intricate wiring and more complicated workflow to the temperamental camera rigs.
Demons in the Dark: Creature Design: In the second section we see the pre-production design of the monsters; here, we get to see the on-set, practical aspects of bringing the monsters to life using "cable technology"—that is, animatronics—and "good old fashioned movie tricks." For example, you'd never know the amniotic sac of the alien inside Shaw is just a condom.
Hazard Pay: Stunts and Action: Lots of juicy behind-the-scenes footage of the film's intense stunt sequences, especially the lengthy fire burns, the engineer fight scene, and the climax.
Fire from the Sky: Visual Effects: Not everything was done practically of course, and this section explores the digital effect work from Weta Workshop and others, from the decomposition of the engineer at the beginning to the creation of the alien landscapes, the creatures, the med-pod scene, and the birth of the "deacon."
Prometheus Unbound: Post-Production and Release: The first part of this section is all about the polish. The editing process with Pietro Scalia. The decision to go for the R rating. The scoring at Abbey Road. The sound design. Then we go to the internet hype machine and the fans. In a particularly revealing moment, Lindelof admits,"Will it be frustrating at the end? Absolutely. Be we all agreed that that was a good thing for it to be."
Enhancement Pods (1080p, 1:10:54): If a nearly four-hour documentary weren't enough, there are twenty-three "enhancement pods," which go in-depth into subjects that aren't fully covered in the documentary proper, including the titling of the film, the role of sex, the set decorating, the evolution of the Weyland logo, the creation of the "ampules," Giger's influence, the construction of the engineer language, shooting on location in Iceland, and more. You can trigger these from within The Furious Gods—an icon appears onscreen at key junctures—or select them from the main menu.
Weyland Corp Archive: Everything else goes here, in the Weyland Corp Archive, where you'll find image galleries, pre-vis animatics, screen tests, promo featurettes, and marketing materials, with sections for pre-production, production, and release.
The Art of Prometheus (1080p): A series of galleries, with sections for Ridleygrams, Giger & Gutalin, Conceptual Art, Costume Design, Creatures, Vehicles, Props, Logos & Patches.
Pre-Vis (1080p, 25:47): Pre-vis animatics for several key sections through the film.
Screen Tests (1080p): Here you'll find Noomi Rapace's initial test as Shaw (9:55) and a Costume/Make-Up/Hair test with optional cast commentary (11:28).
Time-Lapse Sequence: Juggernaut (1080p,1:51): A time-lapse of the construction of the "pilot's chamber," with optional commentary by production designer Arthur Max.
Unit Photography (1080p): Galleries of on-set/on-location images, with sections for Prometheus, Pyramid, Juggernaut, Creature Shop, and Iceland.
Marketing Gallery (1080p): With sections for Poster Exploration and Key Art.
Trailers and TV Spots (1080p): Here, you'll find two US trailers, an international teaser, and a whopping twenty-eight TV spots.
Promotional Featurettes (1080p, 18:43): Nine hype-building promos, featuring on-set footage, brief clips from the film, and the cast and crew talking up the movie, discussing the characters and the story's themes.
HBO First Look: Prometheus (1080p, 12:03): A short HBO special that's basically an extended version of the previous featurettes, introducing the film's key concepts and featuring interviews with Ridley Scott and members of the cast.

One of the 1 star reviews on Amazon.com says he's giving it the 1 star simply due to the fact that you have to buy the 3D version to get all the extras. The rating had nothing to do with the movie itself, just the included content. I haven't seen a listing of what the difference is, and he doesn't say either, so take that for what it's worth.

Amazon has the 3D pack for $25 ("normally" the price is $50, it says it is a 4 disk set), the regular BD/DVD pack for $20 (2 disk), and the DvD for $12 (one disk).

the two disks in the BD are obviously the BD on one disk while the DVD is on the other, but what are the other two disks in the 3D pack? one is obviously the 3D version, but the fourth?

is it just that the 3D is so damned big that it takes two BDs, or is it another disk of extras?

Nevermind, 3D set has a lot more extras:


2D Blu-ray Disc

Audio Commentaries
Director/Producer Ridley Scott: If you're like me, you could listen to Scott talk about his work for hours, and he thankfully obliges us here with a detailed commentary that takes us through the nuances of production, from the decision to revisit the world of Alien to the casting process to the joys and challenges of shooting in 3D. Great stuff, even if Scott sometimes lapses into describing—in great detail—exactly what's happening on screen.
Writer John Spaihts and Writer/Executive Producer Damon Lindelof: I have the unsubstantiated feeling that Spaihts resents Lindelof's involvement—the latter was brought in to rework the former's script—and so I wasn't surprised that this is one of those patchwork commentary tracks where the two participants are recorded separately and their remarks edited together later. Still, there's so much to learn here about the creation of the story, the teasing out of the film's themes, and the development of the characters. Well worth a listen.
Deleted and Alternate Scenes (1080p): Ridley Scott and editor Pietro Scalia have put together nearly 37-minutes of deleted/extended/alternate scenes, most of which are small character-building beats. There are a few small revelations here, though—nothing game changing—that give insight into the world of the engineers. Each scene features optional commentary by Scalia and visual effects supervisor Richard Stammers. Below I've included the scene descriptions that are included on the disc; tread lightly, there are spoilers ahead.
Arrival of the Engineers (2:45): "The engineers touch down on Prehistoric Earth for a sacred ritual devoted to the seeding of intelligent life. Whereas the theatrical version of the scene is devoted to the lone sacrificial engineer, this early cut features several of his comrades, including the elder engineer. The ceremony was filmed with dialogue but unsatisfied with the result, Ridley Scott removed the recorded dialogue entirely."
T'is the Season (1:07): "Janek and Vickers test each other a bit on Christmas morning in this extended scene." With optional commentary by Scalia and Stammers.
Our First Alien (00:51): "Biologist Milburn makes an exciting discovery in the engineer pyramid which could very well represent the first stage in the evolution of a far more dangerous organism. David seems pleased."
Skin (00:51): "Milburn and Fifield make an odd find (which may strike a chord with Alien fans) in the pyramid. Could it be a clue as to what killed off the engineers?"
We're Not Alone Anymore (1:32): "Following the team's return from the engineer pyramid, Shaw shares a toast with the Prometheus crew, celebrating their historic discovery. Holloway does not share her enthusiasm."
Strange Bedfellows (3:11): "In this original version of the scene, the tension between Shaw and Holloway is significantly more argumentative, resulting in a less-sympathetic depiction of Holloway and undermining the impact of his eventual fate. This scene was reshot months later with the version that now appears in the film, taking a softer, more romantic approach while establishing that Shaw is infertile, better setting up the horrific revelation that is to come."
Holloway Hungover (1:35): "An extended version of the post-coital scene in Shaw and Holloway's quarters, allowing the couple a few more tender moments together before unknowingly beginning what will be their final journey together."
David's Objective (00:31): "This brief transitional scene increases the tension between David and Vickers as she suits up to intercept the infected Holloway and defend the ship from possible contagion."
Janek Fills Vickers In (3:43): "Following Holloway's demise, a shaken Vickers is visited in her quarters by Janek, who attempts to console her. He then tells her about his military history, adding a tale that seems to parallel what the engineers might have been up to."
A King Has His Reign (3:56): "An extended version of this uneasy reunion between Weyland and Vickers, this scene includes additional dialogue. This moment, along with 'Fifield Attacks' and most of the connecting scenes between them, had their order significantly restructured deep into the editing process for greater story clarity."
Fifield Attacks (2:14): "Originally intending to show Fifield's mutation in a more advanced stage, the visual effects team at Weta planned on using on-set footage of actor Sean Harris and his stunt double Will Willoughby in full prosthetic make-up as reference and later replace them with a completely digital creation. In the end, Ridley Scott opted to 'keep it real' and use Harris' live performance instead of this alternate CG version of the scene. Yet another alternate cut of this scene in which Weyland, Shaw and team were to leave for the engineer pyramid in the midst of Fifield's attack (glimpsed briefly in the film's trailers) was abandoned early on."
The Engineer Speaks (4:23): "Awakened after two-thousand years of hypersleep, the Engineer is greeted by Weyland and the others. David's study of ancient languages comes in handy as he serves as Weyland's interpreter."
Final Battle (5:51): "Shaw returns to Vickers' escape vehicle to regroup, only to be tracked there by the furious engineer. The final confrontation between Shaw and the engineer was originally intended to be a slower burn leading up to a longer, more physical clash between the two, as scene here."
Paradise (5:20): "This extended scene reveals new information about the engineer homeworld as well as some alternate dialogue between Shaw and David. Note that one of Ridley Scott's original titles for the film was Paradise and it was even maintained as a cover title for secrecy during production."
The Peter Weyland Files (1080p, 18:57): A collection of internet promo videos, presented within a dossier of sorts, with notes from Weyland, the most revealing of which suggests that Weyland's scientists detected a signal coming from LV-426—the moon from the first Alien film—and that Weyland considered it a secondary objective. There's also a potentially interesting connection made to Blade Runner's Eldon Tyrell, which could suggest some sort of crossover in either the Prometheus sequel or Ridley Scott's upcoming new Blade Runner film. Or, of course, it could just be there to tease us.
Quiet Eye: Elizabeth Shaw: A video call Shaw made to Weyland to introduce herself and explain her findings.
Happy Birthday, David: An introduction to the 8th generation android, David, who explains what he thinks about and what makes him sad.
Prometheus Transmission: A collection of pre-mission "interviews" with the crew of Prometheus. The crew of the ship, that is, not the film.
TED Conference, 2023: In the best promo, a young Peter Weyland—Guy Pierce, sans old man makeup—gives a darkly inspirational TED Talk where he proclaims that "we are the gods now" and "if you'll indulge me, I'd like to change the world."


Source: http://www.blu-ray.com/movies/Prometheus-3D-Blu-ray/39474/#Review

ahhh, K, that helps ....

Does anybody know what, if any, bonus features are on the standard DVD?

3... 3D?
KILL IT WITH FIRE!!
NUKE FROM ORBIT!!!