I'm primarily interested in the storyline differences between special sets and their theatrical counterparts, so here are the differences between the two (NOTE: SPOILERS FOLLOW).

The extended collector's edition runs 16 minutes 28 seconds longer than the theatrical cut, and listed below are the major differences.

1) The opening scene is different, and starts with Jake in a wheelchair on Earth, in a Blade Runner-esque Earth city. The scene moves to scenes of Jake in his apartment, then taking liquid shots in a bar. Jake's narration of "I told myself I can pass any test a man can pass" and "They can fix the spinal if you got the money. But not on vet benefits, not in this economy" are inserted during this new opening scene.

Jake beats up a bar patron who is mistreating a woman, and then Jake and wheelchair are unceremoniously thrown outside by bouncers into an alley. While in the alley, Jake meets the two RDA representatives who bring him news of his brother's untimely death. Then the movie cuts back to the original theatrical cut where Jake sees his brother's body cremated, then awakes in space.

2) During Jake's initial flyover of Pandora in his avatar, they witness a herd of Sturmbeasts, buffalo-like creatures.

3) After seeing the Sturmbeasts, Grace, Jake, and Norm stop by Grace's old English school for the Na'vi. The school is now closed, abandoned, and some walls are riddled with bullet-holes. Norm finds a Dr. Seuss book, "The Lorax", on the ground. This scene explains how Neytiri knew English so well, and certainly gives some further backstory into Grace Augustine's character.

Interestingly, The Lorax can be seen as a metaphor for the Pandoran story. Recall that the seemingly simple Seussian book is actually a lesson on the plight of the environment and industrialization.

4) We see some other different Pandoran flora and fauna, particularly with scenes of the luminescent forest floor.

5) Jake's first dinner with Neytiri is longer and extended, and it's here that she tells him her full name.

6) When Jake, Grace, and Norm first visit the Hallelujah Mountains on the way to the remote uplink station, Grace explains (in a Jake voiceover) that the mountains are levitated [via the Meissner Effect], because Unobtanium is a superconductor. There's a pretty spectacular CGI shot as the characters look around in awe at the suspended mountains.

7) Pictures of Grace and Na'vi children at her previously functioning school. Dr. Augustine tells Jake that she previously taught Neytiri and her sister, Sylwanin. However, one day, Sylwanin and some hunters destroyed an RDA bulldozer, and RDA SecOps troopers killed them at the school, which explains why the school walls were previously seen pockmarked with bullet holes.

8) Sturmbeast hunting scene after Jake tames a Banshee. After Jake successfully kills a Sturmbeast with an arrow, he and Neytiri chortle a "Heck yeah!" and whoop.

9) Jake and Neytiri's love scene comprises them linking braids together. Some kissing, nothing explicit.

10) Tsu'tey leads a war party that destroys the RDA's autonomous bulldozers, as well as the RDA SecOps squad that was guarding them. Corporal Wainfleet leads the search party that uncovers the evidence, via real-time helmet cam footage. Not sure why they cut this scene from the theatrical cut, as it persuades Selfridge to attack the Home Tree.

11) Attack of Hammerhead Titanotheres on RDA forces has been extended slightly; additional scenes of AMP-Suits getting destroyed.

12) Fight between Colonel Quaritch in AMP Suit and Neytiri on Thanator slightly longer.

13) Tsu'tey's death scene; in the theatrical cut, he falls off the RDA shuttle's aft ramp to his death. In the Collector's Edition, he falls to the forest floor, mortally wounded. He passes on leadership to Jake, and asks Jake to ceremonially kill him e.g. hara-kiri, so that Jake will be the last shadow that Tsu-Tey sees. Jake does so.

I preferred the original Tsu'tey death scene, which was more dramatic. Jake, had afterall, already become the de facto clan leader by that point in the movie, so further formal transfer by Tsu'tey (a minor character) seemed unnecessary.

I got this as soon as I found it available on the net. It will not be available commercially for some time and that, of course, means the price is WAY to high for most viewers. I was willing to be taken for a ride but if you do not just have to have it now I would recommend waiting until it is available everywhere.
The video quality is fantastic. I have a Samsung 40" 3D setup and the movie was just beautiful to watch. Not quite the same as IMAX but very close (size of screen being the only difference that I could see). The 3D is, to my eyes, exactly as good as the IMAX on-screen version. I am a huge fan of the movie but believe me I would tell you if the video quality was not great.
I would not hesitate to do the purchase again (even considering the huge rip-off in price at this time) but advise others to consider if you really have to have it right now or can wait awhile.
Great movie, almost unbelievable video transfer quality, and a price that is just not right!
Hope this helps.

There are many low score reviews purely based on the fact there was a release of this movie earlier this year and now the extended version comes out feels like a marketing game. When the first release happened it was known an extended version was coming, but some people just had to have it now. I just watched it on Netflix and waited for the extended version. I agree if you bought the first release version you have little real reason to buy the extended version, unless you love this movie and want the bonus features.

Some of the other low scores talk about the 3D version coming, but that is weak reason for most people because most do not own and will not own a 3D TV set. If you do your research on 3D TVs you will find they clunky and costly. Unless you are among the few who have a 3D TV, then there is no reason to wait to buy this release of Avatar if you enjoyed the movie.

For the few who have never seen the movie, the key factors to consider is if you are a science fiction fan, enjoy action movies, and if you consider yourself picky about dialog/originality, Avatar breaks no new ground when it comes to story, but it does take many of successful elements from other stories and rolls it into this one. The bashing on acting is overkill. In general they did a fine job, not exceptional, but anyone who loves science fiction will find the acting a step above the normal for this type of movie. The dialog is nothing special. There are mostly cliche characters and situations. The key is the entire package is very well done. No movie is perfect and as much as some people bash this, just look at the box office sales. Bad movies would have never set top sales records no matter how much marketing was behind it. This movie is not for everyone, but it is good to great entertainment for many.

BOTTOM LINE: If you loved the movie and do not own it, you might want to get this. If you have never seen the movie, rent it or barrow it first. It is a science fiction classic worth consideration for most people.