A Study in Scarlet: Holmes being taken aback and flattered at Watson's praise of his detective skills, contrasting sharply with Lestrade and Gregson alternately sneering at his ideas and being resentful when he is right.
"...all facts which led me to believe that he had been a sergeant.”
“Wonderful!” I ejaculated.
“Commonplace,” said Holmes, though I thought from his expression that he was pleased at my evident surprise and admiration.
And then later that same day:
"You know a conjurer gets no credit when once he has explained his trick; and if I show you too much of my method of working, you will come to the conclusion that I am a very ordinary individual after all.”
“I shall never do that,” I answered; “you have brought detection as near an exact science as it ever will be brought in this world.”
My companion flushed up with pleasure at my words, and the earnest way in which I uttered them. I had already observed that he was as sensitive to flattery on the score of his art as any girl could be of her beauty.
The Sign of the Four: Holmes plays Watson to sleep with his violin.
Watson and Mary holding hands outside Pondicherry Lodge, and confessing their love for each other, also after they open the jewel-box, with an especially touching speech by Watson:
"Because you are within my reach again," I said, taking her hand. She did not withdraw it. "Because I love you, Mary, as truly as ever a man loved a woman. Because this treasure, these riches, sealed my lips. Now that they are gone I can tell you how I love you. That is why I said, 'Thank God.'"
"Then I say 'Thank God,' too," she whispered as I drew her to my side.
Whoever had lost a treasure, I knew that night that I had gained one.
The Three Garridebs: When Watson is shot, we see what may be the only instance in the canon of Holmes truly shaken. "You're not hurt, Watson? For God's sake, say that you are not hurt!"
Watson's commentary clinches it:
It was worth a wound — it was worth many wounds — to know the depth of loyalty and love which lay behind that cold mask. The clear, hard eyes were dimmed for a moment, and the firm lips were shaking. For the one and only time I caught a glimpse of a great heart as well as of a great brain. All my years of humble but single-minded service culminated in that moment of revelation.
And, just to wrap it all up, we have this:
"By the Lord, it is as well for you. If you had killed Watson, you would not have got out of this room alive..."
The Devil's Foot: Holmes loses his composure after Watson has saved them both from the titular drug/nerve gas and admits that he should never have subjected his friend to it.
The ending of The Yellow Face when Grant Munro decides to accept his wife's biracial daughter into the family.
Grant Munro: I may not be a very good man, Effie, but I think I am a better man than you take me for.
This is even a CMOH in-universe; Watson prefaces it by saying that just thinking about it gives him warm fuzzies.
And don't forget what Holmes says at the very end: "Watson," said he, "if it should ever strike you that I am getting a little overconfident in my powers, or giving less pains to a case than it deserves, kindly whisper 'Norbury' in my ear, and I shall be infinitely obliged to you."
This troper believes that the whole passage is necessary in order to fully comprehend the true power of this scene. It's not just Munro, it's not just Holmes, it's Watson's narration:
It was a long ten minutes before Grant Munro broke the silence, and when his answer came it was one I love to think. He lifted the little child, kissed her, and then, still carrying her, he held his other hand out to his wife and turned towards the door.
"We can talk more comfortably at home," said he. "I am not a very good man, Effie, but I think that I am a better one than you have given me credit for being."
Holmes and I followed them down the lane, and my friend plucked at my sleeve as we came out.
"I think," said he, "that we shall be of more use in London than in Norbury."
Not another word did he say of the case until late that night, when he was turning away, with his lighted candle, for his bedroom.
"Watson," said he, "if it should ever strike you that I am getting a little over-confident in my powers, or giving less pains to a case than it deserves, kindly whisper 'Norbury' in my ear, and I shall be infinitely obliged to you."
The Empty House: Holmes explains that part of the reason he chose to reveal himself now is because he learned of the death of Watson's wife, and "Work is the best antidote to sorrow, my dear Watson."
The entire first half, where Watson tries his own detective work. Just... bless him.
Another The Empty House example: Holmes and Watson's conversation after Watson woke up from fainting due to Holmes' sudden reveal of being, y'know, alive. It's an incredibly sweet moment, as they're both concerned for the other's wellbeing in their own sorts of ways...
The Six Napoleons where Lestrade and Holmes are finally reconciled.
"'We're not jealous of you at Scotland Yard. No sir, we are very proud of you, and if you come down tomorrow, there's not a man from the oldest inspector to the youngest constable who wouldn't be glad to shake you by the hand.' 'Thank you!' said Holmes and as he turned away it seemed to me that he was more nearly moved by the softer human emotions than I had ever seen him.
Not to mention Holmes getting all soft-hearted when Watson and Lestrade heartily applaud after he presents the pearl.
The Solitary Cyclist: Carruthers throws the entire evil plan away out of love for Violet in his confession
At the end of The Blue Carbuncle, which takes place during Christmastime, Holmes and Watson finally corner the man who stole the jewel. After admitting everything and falling completely apart for guilt, Holmes, seeing that jail would ruin his mental state completely, lets the culprit go free.
A Scandal in Bohemia: Holmes tells Watson, "I am lost without my Boswell."
In The Lion's Mane, Holmes is on his own, having retired and moved to the country while Watson stayed in London. They see each other on weekends, but it's clear that the detective misses his Boswell.
In The Man with the Twisted Lip, where Watson goes to retrieve a patient from an opium den and runs into Holmes there. It's quickly revealed that Holmes was only working a case, but Watson's initial freakout shows how much he cares about his prickly partner.
John Farrier and Lucy in A Study In Scarlet. He looked after her in terrible conditions, even adopting her once they were rescued and settled with the Mormons. And he was willing to kill, and to die, to protect her. The fact Doyle took the time to establish that Lucy had grown into a happy young woman and that her father was a decent man made the whole business even worse.
In The Dying Detective, we see Watson ready to go to any lengths to save his friend's life, even if it means catching Holmes' disease and possibly dying himself. For his part, Holmes has a Freak Out when he sees Watson touching a box on his mantlepiece; we later find out that the box contained the disease and would have killed him.
The moment in The Bruce-Partington Plans when Holmes and Watson discuss breaking into a house; also a Moment of Awesome.
"I don’t like it, Holmes."
"My dear fellow, you shall keep watch in the street. I’ll do the criminal part. It’s not a time to stick at trifles. Think of Mycroft’s note, of the Admiralty, the Cabinet, the exalted person who waits for news. We are bound to go."
My answer was to rise from the table.
"You are right, Holmes. We are bound to go."
He sprang up and shook me by the hand.
"I knew you would not shrink at the last," said he, and for a moment I saw something in his eyes which was nearer to tenderness than I had ever seen. The next instant he was his masterful, practical self once more.
Bit of Fridge Brilliance and the series' famously inconsistent continuity here... but in The Blue Carbuncle Holmes says Watson is his only friend. His letter to Watson in The Final Problem mentions regretting the pain his death will cause his friends, implying Character Development.
Granada TV series
After his dramatic reappearance in The Empty House, Holmes stretches out on Watson's exam table for a nap and, completely exhausted from his long flight, is asleep in seconds. Watson looks down at him for a moment, shakes his head, then pulls the blanket over his friend.
Shortly before that there's Watson revealing he had Holmes' final letter framed and hanging on a wall. Holmes is touched to the point of speechlessness.
The Empty House : More of a tearjerker really, but knowing that Jeremy Brett's Wife really died before filming, makes his in universe advice to Watson after the death of Watson's wife, "Work is the best antidote to sorrow, my dear Watson.", guaranteed to see even the stiffest lip reduced to a quiver. note Watson never married in the Granada 'verse, and so Holmes doesn't say it.
The moment in The Devil's Foot when Watson saves himself and Holmes from the titular drug, Holmes, having lost any composure he had, calls Watson 'John' for the first and only time.
The exchange (detailed above) between Holmes and Lestrade at the end of The Six Napoleons, played pitch-perfect between Jeremy Brett and Colin Jeavons.
The exchange (and kiss) between a disguised Holmes and the Milverton housemaid in The Master Blackmailer. Sure, Holmes is only going along with the romance for espionage purposes, but judging from his reaction it's hard to believe he's completely faking it in that scene.
Holmes: (voice breaking) Oh, Aggie... you've touched my heart.
Aggie: (tenderly) Oh? I can make you a gift of mine.
Guy Ritchie film series
When Mary was seeing to a very injured Watson, she asked the doctor how Watson was doing. The doctor excused himself, and she asked him if that was the best he could do. Mary figured out that the doctor was Holmes. Without verbally acknowledging his true identity, she comforted him and told him that Watson had gone into this willingly and saw it as an adventure, and she encouraged him to try to fix this situation. Knowing Holmes, he would know that she knew who he was, making it an important moment of understanding between the two of them.
The moment in 2009's Sherlock Holmes when Holmes very awkwardly tells Watson that he's glad he survived the explosion.
And when, having spent the entire movie subtly and not-so-subtly trying to break up Watson and Mary, he donates a big-ass diamond (liberated from Irene Adler, who in-turn liberated it from an Indian maharaj) for their engagement ring.
The Reveal that Lestrade believed Holmes about Blackwood's plan to take over, and gave him the key to his cuffs.
The departure of Irene Adler at the end of the first film:
Irene: (with tears in her eyes and one running down her cheek, smiling) You'll miss me, Holmes.
Sherlock: Sadly...yes. (he wipes away her tear and kisses her forehead before getting up to leave)
Kicked into Tear Jerker status in the reveal of her fate in Game of Shadows, where this exchange is retroactively given a great deal more weight.
Holmes and Clarkie, an officer, have something of a friendship throughout the movie, and when a warrant is put out for the former's arrest, Clarkie finds Holmes, assures him Watson will be fine, and orders him to disappear before the others find him.
Sherlock Holmes: A Game of Shadows
In Game of Shadows, the look of relief on Watson's face after Holmes un-dies after Watson injects him with the serum Holmes gave him as a wedding present was quite touching.
And his attempt at CPR before that.
You selfish bastard!
Sebastian Moran, for all his wicked deeds, cares deeply enough for Moriarty that he digs him out of a huge pile of wreckage after nearly being killed himself.
In one scene from A Game of Shadows, Watson rushes to the side of a bloodied Holmes. In an interesting combination of Call Back and Tear Jerker, Holmes, who has just been brutally tortured and had a building collapsed on top of him, smiles up at him and weakly declares, "Always good to see you, Watson."
At the end of the second film, you can see quite a large number of people attending Holmes' funeral. Even Inspector Lestrade shows up!
The Baker Street Irregulars in the front row.
Noticing even the people who showed dislike for Holmes are heartbroken, Lestrade and Mrs. Hudson are some of the more obviously distraught attendees of the funeral.
Watch carefully during this scene. Notice that there are so many people in the church, there's no room to sit. For all the talk of Holmes being an antisocial misanthrope, so many people respected him, they could barely fit them all inside.
Holmes at Watson's wedding looking happy for him especially if you remember the last film.
Also Holmes helping Watson into the church because he's lost his cane.
And when Holmes managed to drag the hungover Watson and helped him get ready.
The ballroom scene, Ho Yay aside, it is genuinely sweet to see Holmes and Watson not bicker for a change and smile and get along. This may be a Tear Jerker considering what happens next
Holmes keeping the wedding rings for Watson because he knows he has a gambling problem and might lose them is a beautifully subtle acknowledgement of how well these two men know and care about each other.
"If the detective should suffer overmuch from the artistic temperament, and his fellow lodger should dwell overlong upon the fairness of a wrist or the timber of a feminine voice, so much the better for us. Literature never produced a relationship more symbiotic nor a warmer and more timeless friendship." — Loren D. Estleman