Compared are the cut version Lost: The Complete Collection (BD) and the uncut version Lost: The Complete First Season (DVD).

On May 25, 2005 the finale of season 1 of "LOST" premiered, "Exodus, Part 2".
It's a two-hour episode which was cut into two parts for later broadcasts, foreign markets, as well as Netflix and Hulu, respectively: "Exodus (Part 2)" and "Exodus (Part 3)"
On September 6, 2005 "Lost: The Complete First Season" (DVD) was released. It contains the original version of the season finale with a running time of 84:58 min.
On June 16, 2009 "Lost: The Complete First Season" (BD) was released. This set features only the two cut parts. The same applies to "Lost: The Complete Collection" (BD) and "Lost: The Complete Collection" (DVD) which were released on August 24, 2010.
These cut parts have a running time of 43:09 and 43:24 min, respectively. So taken as a whole they are actually 95 s longer than the original version.
This comparison clarifies the differences between both versions for the first time. They not only include cuts, but also alternative material as well as a changed order of scenes and a slightly less cropped image.
These differences may not be significant but my conclusion still is that both versions are necessary for a complete collection!

12 changes = +119 s

0:00 - 1:41 min
"Exodus (Part 3)" begins with an additional "Previously on Lost" segment:
- Danielle warns the survivos of the Others. ("Exodus, Part 1")
- Jack explains his plan. ("Exodus, Part 1")
- Leslie Arzt dies. Jack, Locke, and Kate discuss who will carry the dynamite. ("Exodus (Part 2)")
- Danielle asks Claire to hold her baby. Sayid and Charlie chase Danielle. They rest next to the plane wreck of the Nigerian drug smugglers. Sayid mentions it has loaded heroin. ("Exodus (Part 2)")
- Hurley and Locke discuss what's inside of the hatch. ("Exodus (Part 2)")
Difference: +101,8 s

1:41 - 1:45 min
The scene where Jack, Kate, Locke, and Hurley walk through the jungle is shown from a slightly different perspective and a different take is used. In addition to that the music is missing here which continues from the previous scene in the original version.
No time difference

Blu-ray	DVD

3:08 - 3:25 min
The opening credits follow and continue over the following scenes.
In the original version a black screen is shown for about 4 s at this point.
Difference: +12,9 s

8:17 min
A short scene of Sayid running in front of Charlie through the jungle is missing.
Difference: -1,7 s

Blu-ray	DVD

9:33 min
Charlie presses the towel on his wound for a shorter time. In addition to that Sayid's urgent line is missing: "Remove the towel!"
Difference: -2,1 s

Blu-ray	DVD

15:59 min
Kate contemplates for a shorter time before replying to Hurley's question about the number 23.
Difference: -1 s

Blu-ray	DVD

16:09 min
Kate looks at Hurley for a slightly shorter time.
Difference: -0,6 s

Blu-ray	DVD

19:22 - 19:24 min
An additional black screen is inserted.
Difference: +2,3 s

19:24 - 20:51 min
Locke's flashback to the airport is shown already now, i.e. after Locke's statement that Jack also believed in destiny even though he didn't know it, yet.
In the original version this flashback is shown only after the nightly scene on the raft.
No time difference

22:17 - 24:31 min
Only now the nightly scene on the raft follows here, i.e. after Kate runs the fuse.
In the original version this scene is shown already after Locke's statement that Jack also believed in destiny even though he didn't know it, yet.
This is the original order of the scenes in question: Locke's statement, raft, Locke's flashback, fuse, black smoke
This is the order shown on the Blu-ray: Locke's statement, Locke's flashback, fuse, raft, black smoke
No time difference

27:30 min
Jack carefully lifting a stick of dynamite is missing.
Difference: -2 s

Blu-ray	DVD

42:36 - 43:24 min
"Exodus (Part 3)" ends with the closing credits which are longer than those of the uncut episode.
Difference: +9,3 s

In addition to that I noticed that the Blu-ray shows a slightly less cropped image than the original version on the DVD.

Blu-ray	DVD

Blu-ray	DVD

Thanks a lot to Muck47, TonyJaa, and Cruel_Hides for their helpful support!