They had a lot of Joel Goldsmith's score in it, which was nice.
They did add some new effects, particularly of the kawhoosh and the event horizon. And also the trips our heroes took via Wormhole Express were different. Basically they hijacked the Atlantis wormhole just as they'd done in seasons 9 and 10, LOL... They also used a totally new scale model for the wide shot of the Abydos pyramid, and the death glider attacks on Chulak was different. All in all, I didn't have much of a problem with it, except maybe the new wormhole from SGA. It's definitely a departure from the movie, as the original COTG preserved continuity by using virtually the same one (and the show used it up through season 8 I believe).
Chris Judge re-recorded his lines, and in most cases you could definitely tell. Brad Wright tells us in the "Back to the Beginning" featurette that the day they filmed the walk through Chulak (after he helped them escape the prison), it was so cold and CJ wasn't used to having his head shaved, his lips were actually trembling and it made him sound a bit funny. So to remedy that, he had CJ just re-record his lines quite recently. In a few cases it's okay, but in a lot it stuck out like a sore thumb. I mean, this was 12 years ago and the voice of the older and hulkier CJ doesn't seem to match too well with his younger version onscreen. But I'm just picky... *shrugs*
As for stuff they cut out and added in.... They cut out the annoying (IMHO) "just because my reproductive organs are on the outside" line that Sam had. It pretty much just has Jack annoyed that she's a scientist, Sam asking if they have to arm wrestle and that's about it. Except for some rather protracted stares at each other (which seemed pretty out of place to me personally).
They stuck in alternate takes of scenes. Like in the scene where they first confront the kids on Abydos and have the standoff, and Daniel runs in telling them to lower their guns. When Daniel welcomes Jack back, Jack walks past him toward Skaara. In the original COTG, Daniel kind of rolls his eyes as Jack does this. But we don't see that in this version. We do see over Jack's shoulder and Daniel basically grinning as Jack reunites with Skaara.
The MacGyver in-joke is gone as Sam goes ga-ga over the DHD. Instead she says "jury rig." When she notices Daniel and introduces herself, they cut out Jack's "I thought you liked to be called 'Captain'" line (which makes sense since they'd cut it in that earlier scene where they first meet). However, Sam still introduces herself as "Doctor." Daniel gives her a kind of shy smile and a little "Hi." Awwww :D Also, Sha're is close to him in these scenes, and she seems to be looking warily at Sam, like she's keeping her eye on her.
Before they leave, Sha're gives Daniel the big kiss as she did before, but Daniel keeps looking back at the others for a couple of seconds for some reason.
When they go to the cartouche room, Daniel doesn't call Sam "Captain Doctor" but just "Doctor." Sam is shown filming the cartouche as Daniel tells Jack what he thinks this all is (this hasn't really changed much from the original version). There are some different angles of the action going on. The little "finishing of sentences" exchange between Sam and Daniel seems a bit longer.
When Sha're is taken by Apophis there's a bunch of things cut. Especially the nudity.
There's an added scene where Jack, Sam and Daniel are in the briefing room talking to Hammond (about trying to find the coordinates to the planet that Apophis took off to). Daniel is still in his robes and as they're going to leave, Hammond tells Jack to get Daniel some clean clothes because he stinks. LOL.
The Jack/Daniel scene is still intact (where Jack finds him in the SGC corridor and they go back to Jack's place).
The next briefing room scene where Hammond designates the SG teams and Daniel asks to be on SG-1 aren't changed that much. You can tell they use some different takes and they cut one scene a bit shorter (where Daniel insists he has to be on their team... the beginning of his sentence is cut).
Not much is different as they go back to Chulak. What's different is when they're taken to that meeting place and treated as gods before Apophis shows up with Amaunet, Daniel suddenly runs up to Sha're. In the original version, we see him stare at her and go "Sha're?" Then suddenly we see him standing up and going, "Sha're, it's me." But here, after he says "Sha're?" He suddenly runs up and babbles, "Sha're, thank God, I didn't think we'd find you..." before Apophis demands he kneel before his queen.
The scene where they end up in the prison is a bit different. It still opens up on Daniel lying on his back, being roused by Sam, but it's a bit different. In this version, Daniel has his glasses off longer and the scenes with him and Sam are a bit longer. He's insisting that they have to go and find Sha're, but Sam doesn't think it's a good idea and reminds him of her eyes glowing. He's still a bit out of it and coughing from being knocked out by Apophis, and Sam helps him up and tries to comfort him.
Not much is different except again you can tell they use some different takes. When Apophis and Amaunet arrive again, there are some more close-ups on Daniel's face and the poor boy just looks crushed at the sight before him.
Then when Teal'c turns against Apophis to help free them, not much has changed except mostly for CJ's re-voicing his lines.
When they're helping the refugees from Chulak get back to Earth, the shots are a bit different and as Jack tells Daniel to hurry up with getting the coordinates back to Earth, there are close-ups of Daniel's face filled with glee at finding the address. Hee! As soon as I have my screencaps uploaded, I will post them at classic_daniel .
The whole situation with Kawalsky getting snaked was cut. The movie ends on SG-1 looking back at the 'Gate and the whole "She's out there somewhere, Jack;" "I know, so's Skaara."; "So what do we do?"; "We find 'em" exchange before Daniel looks back at the 'Gate and that's the end.
All in all, I liked it. Yes, there was quite a bit of different stuff in it. CJ's re-voicing of his lines was pretty glaring a good deal of the time. Some of the new takes I didn't care for as much as the original ones used. But being a behind-the-scenes junkie, it was interesting to see what sorts of different takes they had available to use. And some of them (like the additional/different Sam/Daniel scenes (I know you knew I'd mention that... *g*) and a few of the Jack/Daniel bits like Jack patting Daniel's shoulder in that added briefing room scene) were pretty nice.
I've probably forgotten a few things, but this is what stood out to me the most. I'll post the screencaps as soon as I have them all done. I'll probably upload them not only at classic_daniel , but also in a photo gallery on my website. When I have that all done I'll post the link here. :)
Lightning's getting a bit close so that's my cue to sign off, lol. Have a good night, all.