During the second anniversary event, the devs, two fan radio channels and the fandom as a whole gathered together to commission the U.S.S. Enterprise-F with her designer, Adam Ihle leading the charge. It says something when the fandom as a whole gathered in Earth Spacedock, in dress uniforms, to celebrate the launching of the next Enterprise. Sadly, there's no permanent recordings of the event (at least publicly).
The end of 'Mind Game' in the Romulan storyline, crossing over with Crowning Moment of Awesome with a bit of Tearjerker from the sheer emotion of it. Before you take the infiltration mission, you are explicitly told that the Romulan Republic simply cannot spare the resources to come and rescue you if you blow your cover. They don't have enough manpower to waste on a suicide mission; if your cover is lost, you will be presumed dead. They weren't lying; however much it may pain them, the Republic does not come for you. Your shipmates track you down on their own. And regardless of the faction you chose, they bring an armada to cover your escape. Solely because you are their captain, and they are not leaving you to Hakeev.
One of the accolade dialogues in Temporal Ambassador gives a great one to the Enterprise-C.
Tasha: She's a beautiful ship. It's a shame we have to destroy her to restore the timeline.
The Preservers. Imagine being a race of incredibly advanced beings with the capability of exploring everywhere in the Galaxy... and being all alone. Then imagine deciding to take your advanced technology and using it to create lifeforms shaped after you and then going into a long cryogenically-aided sleep, hoping your experiments will work. And then, imagine waking from that sleep and seeing your creations finding you, learning that your experiments succeeded. And then, instead of acting malevolently towards them, calling them your "children" and joining with them to see how the galaxy has progressed, because you left it for your "children" to have. Now that is the definition of a Benevolent Precursor.
During the Summer event every so often there's a dance party. Since so many players play it for marks, its not uncommon to see IRL couples dancing together at the event, regardless of race, gender, or species. Daww.
The Klingon missions "Afterlife" and "The Gates of Gre'thor" have you rallying spirits of Klingons who had fallen and lost their honor. Two of those are Doran, the first officer of your first ship, and Jurlek, the captain that you ended up delivering a Klingon Promotion to on said ship. As it turns out, Doran's husband was right about her being in Gre'thor and you ended up imposing a Heel–Face Door-Slam on Jurlek, but convince both of them to aid in as well. When your team arrive at the titular gates, the Klingons join in on attacking the demons there and Doran ends up aiding you in opening the gates. By the time those gates are opened, all of those spirits are gone. You gave them a chance to regain their honor, even the cowardly Jurlek.
From Sphere of Influence, the newest featured episode:
Worf: Send your engineer my regards. Captain Shon: I'll let ChiefO'Brien know.
Note that they're talking about Kirayoshi O'Brien, not Miles. Yes, Worf is still attached to that little baby he and Jadzia used to babysit. Dawwww
He did help deliver Molly.
Since Legacy of Romulus, several Romulan Republic Officers have been assigned to various facilities all over the galaxy from Qo'noS to Earth Spacedock, to Deep Space Nine and in between. Seeing a Romulan couple at DS9's replimat, or a pair of RR officers talking about the stars from Earth looking towards their new home in Tau Dewa, watching the formerly Xenophobic Romulans seemingly in awe and dazzled at the worlds beyond their borders and the people who live there is very touching.
R.R. Officer #1: I never thought I would be sitting here on Qo'noS quietly talking. R.R. Officer #2: See I told you the Klingons aren't that bad.
Dave Rivas' behind the scenes video of him recording Captain Shon, while completely hilarious, also shows how much he really takes being the new Enterprise captain seriously. The sheer giddyness on his face when he mentions he plays Shon really makes it clear.
When you rescue Admiral Quinn, you can ask him how can they trust him as they were just ambushed by a fake Quinn. Quinn tells you that he had his misgivings in promoting you after Vega Colony, but now he admits he made the right suggestion.
The end of the Federation/KDF war and seeing everyone celebrating.
One of the patrol missions in the Delta Quadrant introduces Captain Felczer of the Avenger-class U.S.S. Avenger. It's former Community Manager Brandon "BranFlakes" Felczer, whom the forums just loved.
There's several meta aspects to this cameo that takes this straight up to Tastes Like Diabetes levels of heartwarming.
First, the cameo had been planned long in advanced and the Avenger was going to serve as a recurring crew with Brandon at the lead (some cut dialogue indicates a PVE mission involving Brandon was planned), but when Brandon quit PWE, that had to be scrapped, but the team couldn't bear to cut him out entirely.
Second, fans who know the situation that lead to Brandon quitting (namely the looming death of his Father-in-Law, which occurred days after his wedding, and the birth of his nephew) forced him to give up, what he calls his dream job.
In "What's Left Behind," seeing that even Sela has a heart, mourning the death and conversion in Elachi of her crew and even regretting what she did in Legacy of Romulus by working with the Iconians, just proves that Everybody Has Standards.
When news of Leonard Nimoy's passing came to light, players shuffled all the way to Vulcan to pay their respects. KDF members and Rom-KDF players who couldn't go there hung around the area in Sector Space. Thankfully, Cryptic will put in a memorial somewhere for the man.
They went far and beyond that - there will be statues on Vulcan and New Romulus of Spock, each bearing a famous phrase of Spock's ("Live Long and Prosper" and "The Needs of the Many outweight The Needs of the Few", respectively) at each site respectively and the three main hubworlds will bear a memorial plaque bearing the names of various people who made Star Trek what it is today.
There is a Federation memorial on the mezzanine level of ESD with the names and quotes from all the star trek actors who have passed away.