Watching this unfold again, even after seeing the television version several times was still fantastic. I was on the edge of my seat at the conclusion of this episode as if I had never seen it. There is much detail in the dialog and questions answered in the deleted scenes. You should be able to pick out every cut line and every cut scene if you're at all familiar with the original.
There is only one chapter stop in the entire episode, and that's after the credits - you must watch the "Previously on Battlestar Galactica" each and every time - and I can't even explain why those would be on the DVD.
Still in all, a great transfer, a great job. Makes me want to chuck my UK release of Season One out the window and buy the US version.
* The episode now opens with Starbuck briefing Commander Adama and President Roslin about her planned rescue mission for the Resistance on Caprica. Part of this scene was included in the recap section of "Scar."
* On the way to the hangar deck Adama gives Roslin some details on Admiral Helena Cain, stating that "She's a very young officer on a very fast track. Very smart. Very tough. Very well connected." He also indicates her rank as Rear Admiral: "Fleet promoted her to Rear Admiral over half the Commanders on the list."
* In the same scene crewmembers can be seen rushing to the hangar deck, wanting to see Cain's arrival. Colonel Tigh chastises them, but Roslin recognizes the importance of the event for the crew's morale.
* Admiral Cain orders Colonel Tigh to put his men at ease.
* Admiral Cain recognizes Dr. Baltar when she arrives on Galactica thus acknowledging his status as celebrity before the Cylon attack.
* Adama apologizes to Admiral Cain for the celebration, but she declines and says "It's so good to see you."
* The conversation between Adama, Roslin and Cain in Adama's quarters starts more friendly and only turns sour after the topic turns to the Fall of the Scorpian Fleet Shipyards. Some new facts are revealed:
o The electro-magnetic pulse created by the nuclear detonations shielded Pegasus' survival from the Cylon Dradis.
o Pegasus sustained heavy damage from igniting fuel and ammunition.
o Pegasus' computer network was offline in preperation for the overhaul, thus avoiding Cylon infiltration of the Command Navigation Program.
* Cain voices the opinion that they are lucky to have Dr. Baltar aboard after Adama reports his success in interrogating Sharon, and she wants to make an appointment with him as soon as possible, so that he can work with their Cylon prisoner.
* An entirely new scene where Cain and Dr. Baltar visit Sharon in her cell. Baltar reports that they got Sharon to cooperate without torture by treating her like a human being. Cain is visibly appalled by how well Sharon has been treated and makes a point out of ignoring her, despite Sharon trying to talk to her.
* When Admiral Cain is leaving, Six teases Baltar about her. "She's a hard case isn't she? Just your type Gaius. You have a thing for strong, powerful women." Baltar salutes Cain as she leaves.
* The deck gang around Chief Tyrol and Cally receive spare parts from Pegasus.
* Likewise Lieutenant Gaeta receives star charts, computer updates, and a copy of the Pegasus' digital library to compensate for the data lost in the hard drive wipe during "Flight of the Phoenix."
* A small extension where President Roslin complains that only Galactica received supplies, despite the dire needs of the civilian fleet.
* A few added sentences when Laird visits Galactica for the first time.
* After visiting Gina for the first time, Baltar explains to Cain and Fisk that, in order to make progress with her, he wants Gina to be able to bathe and eat adequately, as well as get cloths.
* Cain replies that Gina's comfort is of no interest to her and reveals that she killed "over 800" of her crew by helping a Cylon boarding party gain access to Pegasus. While not specified, that probably happened during the initial attack and led to her being uncovered as a Cylon Agent. Cain also wonders if Baltar has become too close to his prisoners and lost perspective.
* The scene continues with the known part about Baltar's findings and concludes with Fisk respectfully adressing Baltar as "Mr. Vice President" and Baltar commenting on Pegasus with "It's a lovely ship...Looks very new."
* As Cain arrives in her office, Adama is studying her weapons collection. She explains that she doesn't have chairs because standing is better for her back and that as a side effect meetings go faster when her officers have to stand as well. (Her back problems can be seen in "Resurrection Ship, Part II")
* They go a bit into the difference between Galactica and a Mercury class battlestar. Cain says "The ship's nearly twice the size, needs half the crew". This either refers to the double launchbays or the volume, but not the length.
* When Adama relays Cain's orders to transfer Apollo and Starbuck to Pegasus, he stops Starbuck as she is leaving and warns them "Watch out for yourselves. I think they're gunning for you both." to which Apollo replies "I think they're gunning for all of us."
* Tyrol has learned that he is supposed to be replaced as deck chief, prompting Cally's comment "This is bullshit, Chief!" Laird outs himself as the person who will replace him and Tyrol grudgingly shows him the way to his office. We also learn a new use of "frak": "frakwit"
* The briefing for the recon mission on Pegasus opens with a far longer fly-by establishing shot along the entire length of the ship. Stinger now threatens to throw Starbuck in the brig for her insubordination, but she just replies "I like hack." At the end she demonstratively remains sitting when Stinger orders everyone to stand up before dismissing them.
* The controversial and much discussed rape scene has been restored, so that Sharon is really raped instead of Lt. Thorne being stopped before he can carry out his attempt. The edits however are subtle. First, Thorne quickly pulls down Sharon's pants (this is still heavily implied in the original). Secondly, when Helo and Tyrol arrive in the previously aired version, they look into the cell and it cuts to Thorne letting down his own pants. Now the camera stays outside and Thorne can be seen penetrating Sharon from behind. This lasts only for a few seconds while Helo and Tyrol rush in and attack Thorne. Additionally there are a few more protests by Sharon, her screaming "I'll kill you!" and one shot of Tyrol moving his hands between his head and lap.
* Baltar's last visit to Gina in the episode has a longer opening. Baltar carries in the food and orders the Pegasus officer to unshackle her.
* Before Pegasus is shown to launch her vipers Cain orders the main batteries to be targeted on Galactica and says "May the Gods have mercy on their souls."
(taken from http://en.battlestarwiki.org/wiki/Pegasus_(Extended_Version))
As it turns out, some of my elusive confusion was tempered (I remembered the end of Pegasus being a cliff-hanger, yet here it was, first episode on 2.5...) when I discovered the orginal cut of the show as the last episode on 2.0 (which up until this morning I hadn't even opened). Disregard my earlier comments, Ron D. Moore DID include both cuts in the DVD release. Cool.