Since this seems to be an ongoing thing, I’m going to have a sticky post about it and I’ll just keep it updated.
I’m guessing at the episodes, actually, so if I’m wrong, feel free to correct me in the comments. Also, I don’t know which episodes the last two are from. I’m guessing one of you does!
Rachel and Jessie “Hello 12, Hello 13” from “Hell-o” (S1, E14)
Santana comes out to the Cheerios, from “I Kissed a Girl” (S3, E7)
The Box Scene, cut from “Extraordinary Merry Christmas” (S3, E9)
The Warblers – I Want You Back from “Michael” (S3, E11)
Bridesmaids Scene from “On My Way” (S3, E14)
Mike Chang and Parents from ?
Rachel’s Yearbook Message to Kurt from ?
Deconstructing Glee 
I have a lot of feelings about Santana’s coming out scene. She gets to speak for herself, Brittany says something to her — I would have felt so different about the “I Kissed a Girl” episode if this had been in it. I still would have thought there was far too much of Finn running things, but this would have shown Santana having some agency in coming out to a group she’s one of the leaders of.
I actually don’t think that cutting most of these was a mistake at all in terms of the overall narrative arcs of these episodes. Though I am glad that we are getting to see some of the subtleties we missed in the relationships between characters, particularly Jesse/Rachel and Tina/Mike, who haven’t had a lot of screen time.
Oh, also, I’m fairly sure that the Rachel/Kurt scene is from the season finale – Kurt wears that outfit to sing his goodbye to the Glee club. I imagine the Mike scene is also from the same episode, as we don’t know about him going to Chicago until then. 🙂
While I understand why the other scenes were cut (even though I appreciate the extra insight into characters/ships we don’t see much of), three scenes would have been really beneficial to the overall plots.
1) Box Scene. Okay, so this one isn’t totally *necessary* and I’m sorta justifying it because I really just want to watch the Klaine Show in all its adorable beauty. However, Glee does set up from the beginning of Season 3 this parallel between rachel and kurt ‘s journeys through senior year into New York and furthermore sets up a parallel between Finchel and Klaine in The First Time. This could have been a nice continuation of the contrast between the two “power couple” relationships on the show.
2) Santana’s coming out scene. One of few scenes that give her agency in the whole process and could have marginally saved a frustrating episode.
3) Warblers scene. This whole episode I was rather confused by why the Warblers were suddenly turning their backs on Blaine and following Sebastardian’s lead… Also what does Blaine think of this? We get none of the fallout from Blaine himself about what it means to him that his previous best friends who worshiped his talent are suddenly slushying his boyfriend and stealing their setlist. I especially like this meta conversation an explanation: http://lookninjas.tumblr.com/post/28724194252/holy-shit-blaine-figured-it-out-a-blaine