The Batman Gambit Holmes pulls at the end of "While You Were Sleeping", which involves making up a fake heir to the family fortune and convincing a suspect that he's actually suspicious of someone whom the police have already cleared. Bonus points for staging an assault of a police officer and pretending to be arrested. Damn fine acting, Holmes.
A private detective, who was hired to trail one of the victims, refuses to reveal information pertaining to the case at hand. Holmes takes him aside, pretending to want to know about his office plant, and threatens to reveal the detective's meth addiction in front of Captain Gregson and Detective Bell, especially since the private detective is an old friend of Gregson. The detective then relents.
Even more lovely, he's clearly sympathetic to the detective, and offers the name of the clinic where he'd undergone detox.
In the pilot, Holmes manages to deduce that the victim's psychiatrist husband is manipulating his patient, but is unable to come up with solid proof. After confronting the psychiatrist and receiving a Smug Snake response, Holmes takes Watson's car and smashes it into the psychiatrist's expensive coupe.
In a group therapy session, a grumpy Holmes is mouthing off about how much he dislikes the therapy sessions. Watson, having learned that he puts himself into a trance from the last time they went, threatens to jab a thumbtack into his thigh to keep him awake. The Death Glare on her face wisely shuts him up.
Bonus points as the line she used was an Ironic Echo from when Holmes was trying to determine whether or not the coma a suspect was in was real or not. "Lots of nerve endings there..."
Holmes finding a loophole in Adam Kemper's immunity deal: The deal specifies that Kemper cannot be prosecuted for any crimes committed while working with Samuel Abbott. Holmes, using Abbott's hospital records, is able to prove that Kemper committed one of the murders alone and therefore can be charged.
"Rat Race" gives Holmes two:
Since he hates Wall Street elites, he decides to wine and dine on their expense, having the time of his life.
Captured and held at gunpoint by the killer, Sherlock's about to die. He refuses to dig his own grave, and then when the cops arrive, distracting the killer, Sherlock picks his handcuffs, grabs the killer's taser, and turns the tables. This Holmes hasn't had as many physical moments as his literary or BBC counterpart, but this is a promising start.
"The Long Fuse":
A minor one at the beginning of "The Long Fuse", but Holmes is watching six television sets and reading a book at the same time...and can apparently recite the contents of any one of them at will. Even for Sherlock Holmes, that's pretty impressive.
Also, Holmes deduces that a bombing suspect is innocent based solely on the absence of an oak tree on a battery logo and an old picture of Barack Obama. (Both of which prove that the bomb is four years old and thus, could not have been built by the suspect, who was in prison at the time.)
Joan Watson's increasing awesomeness must be mentioned. Within a few weeks of meeting Sherlock, she's good enough at deduction to realize that her date was lying when he said he wasn't married and a few episodes later that Sherlock has a fear of planes, just through body language cues. She also diagnoses a girl with a relatively rare condition through a minor foot injury.
One of the best yet, from "M.": "You." "Me. Baton!" *WHACK*
Followed by a speech on how studies show how the average man will react to any situation, but he's not an average man. Followed by him stabbing M in the stomach, in the precise way that will avoid hitting any organs, to give himself an alibi when he turns M in to the police.
An offscreen one, for Moriarty. He fooled Sherlock Holmes. He fooled. Sherlock. Freaking. Holmes. Were it not for Moran mentioning his alibi, Sherlock would probably be in jail.
And another for Watson's growth as an investigator. She figured out where Sherlock was because a witness mentioned seeing chalk or powder on his shoes.
Also, the reveal that Holmes filled the brownstone with dozens of weapons.
"The Red Team":
For some people, seeing Holmes finally get called out by Gregson for acting like he's better than people because he's smarter than they are was definitely a moment of awesome, especially when he tried to smooth things over with a rather insincere apology.
As part of that, Detective Gregson's punching him in the gut.
From "The Deductionist": Holmes. Singlestick.
A skill straight from Doyle's canon.
And since he didn't stick to the rules of where to hit in Singlestick, perhaps this is the beginning of Holmes' use of baritsu.
Watson: She gets evicted by her landlord because the person she was subletting to made a pornographic film in the apartment, she quickly discovers proof that the landlord was in on making the films. She uses this to blackmail him for money to put her things in storage and for a couch to replace the one that was violated in the film.
Joan takes out an armed gunman by smashing Angus over his head.
Earlier, telling Rhys if she even thinks he's a risk to Holmes' sobriety, she won't hesitate to turn him in to the cops.
Joan calling out Sherlock after he comments on her period.
Joan: Couching it as a scientific observation totally negates the misogyny.
And when a desperate Rhys tries to get Holmes to fall off the wagon in the belief it will help find Emily, Holmes attacks him, followed later by coolly calling off their friendship.
Watson looks in one of Bell's old files and quickly notices that Bell blew the whistle on a detective who planted evidence during a previous case. This turns out to be the crucial clue leading to the identity of the person looking to frame Bell. Note: This is a clue that Holmes, with all of his deductive skills and observational acuity, did not catch. In other words, Watson just solved the case, by herself, with nothing more than a passing glance at an old case file.
Watson getting back at Sherlock's misguided jump attacks on her by knocking down his wall of locks and then later beaning him in the face with a basketball (he had hit her in the back with a tennis ball).
Bell's brother using his own blood to write that Bell didn't shoot him, figuring out immediately that his getting shot was part of the frame job. And he didn't actually see who did it, but knew it couldn't be Bell despite their tempestuous relationship.
"Deja Vu All Over Again:"
Watson increases her awesomeness rating by solving her first solo case and the murder that Holmes was working on.
The villains of "Snow Angels" get one with their utterly brilliant plan to steal millions of dollars without anyone knowing. Sherlock even says he'd be inclined to let them get away with it if they hadn't killed a man.
Marcus Bell gets one when he goes to interview a brunette female hospital patient, notices a strand of blonde hair on her clothes, is able to determine then and there that the strand is from a blonde wig (implicating her in the robbery) and busts her all by himself.
You have to give some points to the guard at the beginning of the episode: The fact that he managed to get a shot off at all was no small feat considering that he was bleeding to death, but it becomes a CMOA when you remember that he not only got a shot off, he sank a bullet into one of the thieves. This even led to Bell's CMOA above: If the guard had missed, the female thief might never have been caught.
Moriarty effortlessly tricking Holmes into relay an order to Moran to kill himself.
In "Heroine" Watson figures out that Moriarty has fallen for Holmes as much as he's fallen for her and devises the trap that captures her.
The reveal of Moriarty is already cool, but it becomes even more awesome in retrospect. She played a completely different person from herself for two years, presumably while still running her network, utterly flawlessly, and was just gearing up for another long game when Sherlock noticed her missing birthmark. Her scheme in the episode is also damn clever, only failing because Sherlock and Joan were able to catch her at the literal last minute.