The Season 2 Premiere, when he returns from what they assumed what a suicide mission.
John: Well I'm home.
Elizabeth: Yes you are. (They hug).
During the siege at the end of Season 1, Colonel Everett arrives from Earth and takes control of Atlantis, completely cutting Elizabeth out of the command circle. So John immediately refuses to co-operate with Everett until he acknowledges Elizabeth's authority and the respect she earned from everyone in the city...including John himself. Bear in mind John is already in a very vulnerable position as the military previously exiled him to Antarctica because of a black mark and he only assumed command of Atlantis because pity-killed Colonel Sumner. But he doesn't hesitate to stick his neck out for Elizabeth's sake.
Then you have Elizabeth's reciprocating loyalty in Season 2 when General Landry tries to replace John as military commander of Atlantis. She basically tells him to screw it and that John will be remaining her second in command even if she has to call in every one of her connections and get him promoted to do it. After a year watching the pair become leaders together and put everything on the line to defend their city it's incredibly heartwarming to see them protect each other's backs from other forces as well.
Elizabeth's 'bedside manner' in Conversion. She fails miserably to comfort John, but he confides his fears in her anyway.
John: Anything that has you speechless has been concerned.
Elizabeth: Beckett can figure this out. You're going to be fine.
John: You're gonna be fine? You really suck at this whole bedside manner thing Elizabeth.
Elizabeth: I know, I'm sorry.
John: ...But I appreciate the effort.
When John takes the unconscious Elizabeth's hand in the episode "The Real World", despite the risk that he may become infected with the same replicator-nanites that are causing her condition. It takes Ronon and several others to finally pull him away from her.
Rodeney Mckay of all people gets one during the Genii invasion of Atlantis mid-season one. When Kolya threatens to kill Dr. Weir, he doesn't hesitate to step between her and the gun. His realization of what he's just done is pretty funny in itself luckily he manages to argue their worth to Kolya and nobody gets shot, but it was pretty close
"You see, the thing is, Colonel Sheppard and I have sort of gotten into this habit of saving each other's lives, and it's my turn!"
"Sateda" oddly enough, after Carson saves Ronon by killing the Wraith that was attacking him knowing full well that Ronon would most likely be very angry. After Ronon is safe and asks who interrupted his fight, McKay immediately points to Carson, who is very terrifed of what Ronon may do to him. Ronon gives him a man-hug and says thanks... much to everyones surprise.
McKay:...Well, I helped too.
Ronon: (pats McKay on the back) Thanks.
In "The Tao of Rodney", McKay gains supernatural powers after being struck by a machine which will either force him to ascend or kill him. McKay, in an attempt to "release his burden", asks Ronon about the scars on his back left from the Wraith tracking device. Ronon replies that he tries not to let things he can't change bother him. McKay thanks him for the advice and gives him a big hug, and says as he leaves "I hope you don't mind - I just healed them."
The fact that he made sure to check he wasn't about to just erase a 'badge of honour' before healing Ronon's back makes this moment that much more special, as it shows he really does have a respect and understanding of Ronon's nature, and could see how he might view those scars as a mark of pride of his defiance against the Wraith.
The exchange just before everyone thinks McKay is about to die (or ascend) is both heartwarming and funny:
Weir: Rodney, you’re a good person. Know that we love you.
McKay: You love me? Really? All of you?
Sheppard: In a way a friend feels about another friend.
The things McKay does for the other members of the Atlantis expedition: writing a 500 page book about Elizabeth, asking to share the memorial tea ceremony (for the anniversary of the death of her father, which is next week) with Teyla, and complimenting and apologizing to Zalenka.
At the end of the episode, Rodney launches into a technobabble-filled explanation of what he did to undo the acension device.
Ronon: "I have no idea what you just said. But it's good to have you back, buddy." *gives Rodney a big hug*.
When Sheppard is taken by unknown assailants in Travellers, the expedition track his location down but still don't know who has taken him. Ronon sums it up.
Ronon: Does it make a difference? Even if it was a fleet of hive ships, would it stop us from trying to get him back?
From the season 5 premiere:
Teyla names her son Torren John, after her father and Sheppard.
After Sheppard rescues Teyla and her newborn son, she tells Sheppard that she never gave up hope that he would come find her.
There's also a sweet moment when John is piloting a Wraith dart with his team (including Teyla, who had recently given birth) beamed into storage. Caldwell sounds shocked that Sheppard would put a baby into Wraith storage, when the camera pans down to reveal that John is holding the newborn in his arms.
"I love you. I have for quite some time now. Just thought you should know." Especially the Call Back in "Brain Storm".
The final episode: after successfully fending off a Wraith attack on Earth, and nearly burning up on re-entry, the final view off of the main balcony of Atlantis is the Golden Gate Bridge.
Earlier, Woolsey calls Teyla and Ronon into his office and offers them the chance to leave the city before they cross into the Milky Way galaxy.
Woolsey: We've all grown so accustomed to having you here as part of the team, it's easy to lose sight of the fact that your priorities are not necessarily always the same as ours. You're being asked to fly to another galaxy, to take what might turn out to be the losing part in a battle that isn't yours.
Ronon: You mean like everyone on this base has been doing for the last five years?
Teyla: Thank you for your consideration, Mr Woolsey, but I assure you it is not necessary.
Ronon: We're not going anywhere.
The revelation that the Phoenix was renamed the George Hammond in tribute to him, after he (and his actor Don S. Davis) tragically passed away.
In "Adrift", Ronon thanks a comatose Weir for letting him stay on Atlantis because he would probably be dead if she hadn't. Being Ronon, he is extremely adorable and awkward about it.
The final shot of the season 5 episode 'Outsiders', with Carson and Rodney walking out of medical to get lunch together. Its just nice to see them back to normal, with Rodney finally having his best friend back.
A combined fleet of Earth warships, Wraith Hives and Traveler craft joins up for a major attack on the Asuran homeworld. Acknowledged in-universe. Even Carter and Caldwell are moved by the sight of the unlikely alliance.