I watched along with Ariane DeVere's transcript page of The Reichenbach Fall. The snippets of transcript below are taken from there:
http://arianedevere.livejournal.com/30648.html

(I figured I'd include all this detail because,  well, why are we here anyway?) 

Most of the cuts were small clips here and there.  To give context, I'm including parts of real included scenes.  I've surrounded the actual cut dialog or scene description with the tags
[omit:]  means what follows is omitted
[/omit]  means end of the omitted part


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Jim walking through Tower security:

[omit:]security man gives some items back to a tourist.
SECURITY MAN: Put this in your bag, please.[/omit]
(Jim walks through the detector which beeps an alarm.)
SECURITY MAN: Excuse me, sir.

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When Moriarty is escorted to courtroom, they omit his creepy scene where he asks the female guard for the gum is pocket:

[omit:]
JIM: Would you mind slipping your hand into my pocket?
(The officer looks at one of her male colleagues, who nods in agreement. Looking rather uncomfortable, she slides her fingers into Jim’s trouser pocket and pulls out the contents as Jim breathes very close to her face and gazes into her eyes before poking his tongue out. She puts what she has found in his pocket – a piece of chewing gum – onto his tongue and he draws his tongue back in and begins to chew, smiling at her creepily.)
JIM: Thanks.
[/omit]

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After Sherlock is evidently escorted away for contempt of court, the split screen image of him and Moriatry in adjoining cells is omitted:


JUDGE: Keep your answers brief and to the point. Anything else will be treated as contempt. Do you think you could survive for just a few minutes without showing off?
(Sherlock pauses as he gives the question some thought, then opens his mouth.)
[omit:]
Shortly afterwards, a prison officer marches Sherlock into one of the cells under the courts and shoves him inside, slamming the door shut behind him. A recess has apparently been called in the trial and so a little later two more officers walk Jim to the adjoining cell and lock him inside. As if sensing each other, the two men turn and look at the wall separating them. Jim’s expression slowly becomes murderous.
shut behind him. A recess has apparently been called in the trial and so a little later two more officers walk Jim to the adjoining cell and lock him inside. As if sensing each other, the two men turn and look at the wall separating them. Jim’s expression slowly becomes murderous.
[/omit]

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During the  John/Sherlock 'you're doing the look again' sequence,  they leave out the final line:

SHERLOCK: If Moriarty wanted the Jewels, he’d have them. If he wanted those prisoners free, they’d be out on the streets. The only reason he’s still in a prison cell right now is because he chose to be there.
(He starts to pace again.)
[omit:]
SHERLOCK: Somehow this is part of his scheme.
[/omit]


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They omit the judge's 'you must find him guilty' lecture to the jury, interspersed with Sherlock at home murmuring the lines simultaneously:


DEFENDING BARRISTER: Nevertheless, my client is offering no evidence. The defence rests.
(He sits down. Jim purses his lips ruefully at the judge, then turns and looks up to John, shrugging at him.)
[omit:]
Not long afterwards, Sherlock – who chose to stay back at home – sits up sideways on the sofa with his back against the arm nearest the window. Wearing his blue dressing gown over his clothes, he softly recites the only words that the judge can possibly say in his summing-up speech. His recitation is interspersed with the actual words from the judge, and frequently their lines overlap.
SHERLOCK/JUDGE: Ladies and gentlemen of the jury. James Moriarty stands accused of several counts of attempted burglary, crimes which – if he’s found guilty – will elicit a very long custodial sentence; and yet his legal team has chosen to offer no evidence whatsoever to support their plea. I find myself in the unusual position of recommending a verdict wholeheartedly. You must find him guilty.
(Sherlock closes his eyes.)
SHERLOCK (in a whisper): Guilty.
JUDGE: You must find him guilty.
(The court adjourns at 10:42.
[/omit]
At 10:50 John is sitting on a bench just outside the courtroom when the Clerk of the Court hurries out of a side room.)...

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After the scraping the dried linseed oil/floor wax scene,  the sequence with the clip from the outside of the kids' school is omitted:

[omit:]
LONDON. Sherlock and John are in a taxi.
JOHN: But how did he get past the CCTV? If all the doors were locked ...
SHERLOCK: He walked in when they weren’t locked.
JOHN: But a stranger can’t just walk into a school like that.
SHERLOCK: Anyone can walk in anywhere if they pick the right moment. Yesterday – end of term, parents milling around, chauffeurs, staff. What’s one more stranger among that lot?
(A flashback shows one of the school children outside the entrance being embraced by her mother. Other adults and children are all around, and one man walks alone up the steps towards the door.)
SHERLOCK: He was waiting for them. All he had to do was find a place to hide.
[/omit]


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Small cuts in the Molly scenes (gasp!), like her 2nd mention of 'I owe you':


MOLLY: What did you mean, "I owe you" ?
(John walks across the lab on the other side of the bench. Sherlock raises his eyes from the microscope and watches him as he crosses the room.)
MOLLY: [omit:]You said, "I owe you". [/omit] You were muttering it while you were working.



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Odd they leave out 'hell' here,  they leave it in elsewhere...:

Lestrade - What [omit:]the hell [/omit] is this?  Chocolate?


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Some cuts in the Kitty apartment scene, a bit at the beginning, plus a couple lines.


[omit:]:
Kitty Riley parks her car outside her home, gets out and locks the car before walking to the front door.
[/omit]
Opening it, she walks along the hall to the door of her flat, then pauses...

[omit:]
SHERLOCK: Oh, come on, Kitty. No-one trusts the voice at the end of a telephone.
(John finally frees his own hand from the cuffs.)
SHERLOCK: There are all those furtive little meetings in cafés; those sessions in the hotel room where he gabbled into your dictaphone. How do you know that you can trust him? [/omit} A man turns up with the Holy Grail in his pockets. (Sternly) What were his credentials?`

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more unforgivable Molly cuts,  like the mention of her name,  the 'if I wasn't everything you think I am' line,  and her 2nd 'What do you need?':


SHERLOCK (slowly walking towards her): [omit:]Molly,[/omit] I think I’m going to die.
MOLLY: What do you need?
[omit:]
(SHERLOCK (still slowly approaching her): If I wasn’t everything that you think I am – everything that I think I am – would you still want to help me?
(Molly gazes up at him as he stops close to her.)
MOLLY: What do you need?)
[/omit]
(Sherlock steps even closer, his expression intense.)
SHERLOCK: You.



====================================

A line cut from the John yelling at Mycroft scene:

JOHN: So how does it work, then, your relationship? D’you go out for a coffee now and then, eh, you and Jim?
(Mycroft sits down in the chair opposite and opens his mouth but John interrupts again. His voice is full of controlled anger.)
[omit:]JOHN: Your own brother, and you blabbed about his entire life to this maniac.
MYCROFT: I never inten... I never dreamt ...
[/omit]
JOHN (interrupting): So this ...th-th-this ... (he looks through the papers again) ... is what you were trying to tell me, isn’t it: “Watch his back, ’cause I’ve made a mistake."

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The rooftop scene (thank God) was fairly intact.   Perhaps a second or two, or a cut I missed.  Hmm, I
don't remember seeing the birds fly in front of the shot from above of sherlock on stretcher.


====================================
After the rooftop scene,

They cut the short Mycroft scene scene of him and the newspaper at the Diogenes Club,  and John in 221B.   Snipped a bit off the beginning of the final therapist scene too...:

[omit:]
DIOGENES CLUB. Mycroft is holding a copy of “The Sun" . Its headline screams “SUICIDE OF FAKE GENIUS"  and the strap lines state "SUPER-SLEUTH IS DEAD"  and "Fraudulent detective takes his own life". Folding the paper and putting it down on the table beside him, he stares blankly into the distance and then folds his hands in front of his face in the prayer position.


221B. John sits in his armchair, dressed but with his feet bare and tucked together in front of him. One hand is propping up his head and he gazes into the distance, lost and alone.


ELLA’S OFFICE. As the rain continues to pour down, John gazes blankly at his therapist.

ELLA: There’s stuff that you wanted to say ...
(John opens his mouth briefly and then closes it.)
[/omit]

ELLA: ... but didn’t say it.

====================================

Graveyard scene:  intact.   whew.


Though they don't end it with the Sherlock music theme.  It moves straightaway to an ad for an upcoming show,  and different end credit music. It's kind of jarring to not have the theme music take over at the end.  bit not good

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recommended:   watch the DVD!