A lot of work goes into making sure a movie flows well, and sometimes that means great scenes have to be cut out completely. It's not always necessarily because the scene isn't up to par. In fact, many times, some pretty considerable scenes have to be left out.
Cases in point:
Luke Skywalker Lightsaber scene in Return of the Jedi
In this deleted sequence, we see Darth Vader asking Luke to join him on the dark side of The Force. In a simple act of defiance, he tinkers with his lightsaber and it illuminates green, signifying that he's a Jedi.
Jonah Hill's Brokeback Mountain rant from Knocked Up
This hilarious scene could have stayed in my opinion. Jonah goes off on a pretty impressive monologue about how he's upset that Brokeback Mountain didn't feature any male-to-male fellatio. His ironic diatribe is definitely entertaining but may have rubbed a few people the wrong way. Or, at least that's why I'm guessing that they decided to leave it out.
Cap looks back in The Avengers
This scene could've been great. Reminds me of the scene in [Captain America: The Winter Soldier](movie:254973), when he visits Peggy. Steve was an art student prior to becoming Captain America, so the sketching makes sense. Overall, the idea that he's a man out of touch with this new modern society is really cool and would've been a nice addition since that is such a vital piece of his storyline.
Wolverine classic costume scene in "The Wolverine"
I know, I know, this isn't the full scene. However, this is the only time we've seen any kind of semblance of the Wolverine's costume from the comics. It could have been pretty cool to see Hugh Jackman at least try it on once!
This alternate angle from "The Dark Knight"
So, this alternate angle may not qualify as a deleted scene since all of what happens in this scene still happened in the final movie. However, this view of The Joker sitting in his getaway school bus from The Dark Knight after blowing up the hospital is really cool! To be honest, though, I can see why they may have left it out. The scene works without this view just as well, so it all comes to preference.
The Mouth of Sauron from Lord of the Rings: Return of the King
I think that they may have taken this scene of The Mouth of Sauron out due to the fact that it looks like he's wearing a poorly designed "grill". But seriously, the scene follows the framework of Tolkien's book, which I love, but otherwise proved to be dispensable.
Boromir's Story from Lord of the Rings: The Two Towers
I really think this scene could've been kept in the second installment from the LOTR trilogy. It adds a lot of depth to Boromir, Faramir and Denethor. Luckily, the extended version of the film DOES include it.
Lupin and Tonks meet up before the big battle in Harry Potter and the Deathly Hallows — Part II
This scene was only 23 seconds long and could have easily be left in. Many fans think both of these characters were botched in the movies, even though they had big roles in the books. 23 seconds... they couldn't give 23 darn seconds more to these characters? Couldn't they have snuck this powerful and emotional scene into the movie anywhere? I'm thinking that they definitely could have, but what do you think?