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 additional 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 = -23 s

0:00 - 0:03 min
The black screen at the beginning of "Exodus (Part 2)" lasts longer than in "Exodus, Part 2".
Difference: +0,8 s

0:03 - 1:33 min
A shorter "Previously on Lost" segment follows. The missing scenes are:
- Oceanic Flight 815 breaks up and crashes on an island. ("Pilot, Part 1")
- Some survivors try to send out a distress call, but instead receive a message by a French woman which has been repeating on a loop for sixteen years. ("Pilot, Part 2")
- Sayid finds a cable on the beach and is captured by the French woman, Danielle Rousseau. She warns him to watch the other survivors. ("Solitary")
- Claire is attacked in her sleep. Hurley conducts a census of the survivors and determines based on the plane's manifest that one of them wasn't on the plane. ("All the Best Cowboys Have Daddy Issues")

4:32 - 4:35 min
An additional view of the stern of the "Black Rock" is inserted.
Difference: +2,8 s

Blu-ray	DVD

4:35 - 4:52 min
The opening credits start earlier.
Difference: +17,1 s

4:52 - 4:59 min
Locke, Jack, and Kate enter the "Black Rock" one after the other.
The Blu-ray shows this in a wide shot. It offers a slightly different perspective and uses a different take. In the original version the persons are shown individually in a medium close up.
The opening credits continue over the following scenes.
No time difference

Blu-ray	DVD

4:59 min
Locke is shown for a slightly shorter time in the dark hold of the "Black Rock".
Difference: -0,3 s

Blu-ray	DVD

5:04 min
Locke is shown for a shorter time climbing the stairs in the dark hold of the "Black Rock".
Difference: -4,5 s

Blu-ray	DVD

10:45 - 10:47 min
A black screen is inserted.
In the original version the opening credits start only now and continue over the following scenes.
Difference: -15 s

42:03 - 42:08 min
A short scene of Jack looking around before carefully walking on is inserted.
Difference: +4,8 s

Blu-ray	DVD

42:15 min
Hurley walks slightly longer through the jungle.
Difference: +0,2 s

Blu-ray	DVD

42:18 - 42:23 min
With a drum roll "To be continued" is shown.
Difference: +4,5 s

Blu-ray	DVD

42:23 - 43:09 min
"Exodus (Part 2)" ends with the closing credits.
Difference: +46,1 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!