Well, They cut everything that bothered me, and there was nothing cut that I missed.
From the beginning...
Loved the increased film quality and the new sound track. I was really happy with the recut introduction scene with Sam. Now she seems like an officer with enough experience and savvy to be asked to join the SGC, rather than someone who seems rather too green. Now she's confident and knows how to handle the boy's club, not overly defensive.
I was glad to see that Jack no longer walks right through Daniel on Abydos. It seems less like a deliberate slight, and more happiness to see Skaara. I thought the kiss was better, too. It always seemed a bit odd to me that Daniel would be so oblivious to the audience when Sha're kisses him. This is not a guy who's all that comfortable with public displays of affection. Not saying he doesn't like it, he clearly does, but an awareness that they're being watched seems in tune with his character.
I'm a bit puzzled as to how Sam filmed the cartouches when they went all the way to the ceiling, but I'm willing to overlook that. Maybe the important stuff was near the ground. ;)
While the moment of Jack reacting to Daniel's goodbye to the Abydonians was a good Jack moment, I think they were right to cut it. Now we have Daniel delivering a very emotional speech to the Abydonians, saying goodbye, and leaving. Now it's all about Daniel's relationship with the people he has spent the last year with, and about his leaving them. The cut to Jack made it as much about Jack's reaction to that and took focus off that relationship.
I liked it that Hammond pulled them into the briefing room immediately. Had no problem with the extra rudeness of the 'he stinks' bit. To me it showed just how angry he was with Daniel for staying and with Jack for covering it up. He'd had some time to get over his initial anger with Jack, but this was the first he'd seen of Daniel and he was livid. It also gave his character more of an arc over the course of the movie in that he's willing to wait to the last second for them to return, accept the refugees, and take Jack's opinion about Teal'c under advisement. It also made for a very nice moment where Jack is empathizing with Daniel after the total diss from Hammond. And it went a long way in explaining how Daniel comes to be standing out in that hall with no idea of what to do with himself.
The scene between Jack and Daniel at Jack's house really is one of the best scenes in the movie. I never doubted it would be in there for a moment. It's simply wonderful. Great characterizations, a reminder of the friendship they developed on the first mission and I love the way the camera pans out at the end so that we see them sitting in silence, each feeling the same loss of a wife.
I'm so very glad the nudity is gone. I found it utterly exploitive and it really bothered me that they were forced to include it in a show where it so clearly wasn't intended. It's still pretty weird that the female Jaffa carrying Amonet seems to be enjoying the emergence of the Goa'uld so much, but there was nothing they could about that.
I liked the prison scene a great deal, too. Daniel's condition made a lot more sense. He hit the wall incredibly hard--we can see that. He's out for hours, then he just jumps up and is basically fine? This was much better. We see some residual effects. He still recovers quickly, but it's not instantaneous.
I really, really liked the new dialogue for Teal'c. While I've always thought Teal'c was awesome, CJ has come a long way as an actor.
I have no problem with losing Kawalsky getting taken by the Goa'uld, but it does make for some odd scene cuts since, unlike some of the other changes, that editing choice was never on the table in the original. There just wasn't quite enough footage to do that more neatly. Still, that's very minor and I can easily over look it, especially in light of how much improved everything else is.
All in all, very good indeed!
Edit: A number of people have commented on the removal of the MacGyver line, and I have to say that I was pleased by that. I don't mind jokes that remind us that we're watching actors in humorous episodes like Wormhole Extreme or 200, but I don't care for them in serious episodes. To me that pokes a stick at suspension of disbelief. I don't want to be reminded, mid episode, that Jack is played by RDA who was MacGyver. I'd rather just watch Jack.
I've also seen comments, in a few places, that Sam's introductory scene is now 'shippy'. I just don't see that at all. Sam comes across as competent and professional. While it doesn't apply in that particular scene, I also think that the characters can, and should, be allowed to show that they like and admire each other without it being construed as UST or seen as evidence of a relationship. Sometimes people just like each other. :)
As a gen writer, I tend to occasionally omit character interaction and dialogue that I would like to include because I have a sense that it might be misinterpreted and seem to add an element of stealth ship/slash to a story that I want to be entirely gen. That's kind of a shame...