These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
One of the producers commented that its use in the finale was meant to set up the viewers for its use in an upcoming Atlantis movie, meaning that the writing crew tried to pull a Chekhov's Gun out of their ass.
Base Breaker: Rodney McKay. You either like that the smart guy is the one who saves the day or find him incredibly grating.
Crowning Moment of Funny: Doctor Zelenka returning from the planet of the children in "Critical Mass", and Rodney commenting "Mister Mom...fun with the kids?" (He's covered in facepaint and has straws woven into his hair) Zelenka turns to him and says: "Do not even speak to me!"
Designated Hero: although our heroes are in general good guys, there are some episodes where what they do is at the least soaked in Moral Dissonance and at the most downright evil. In "Infection" where Sheppard comes across 'Todd's diseased Wraith hive ship where his entire crew - now having undergone a gene therapy where they can no longer feed - are in stasis pods. However, because of the ship's malfunctions there is an off-chance that they might break free from the pods and attack Sheppard's team and the team of marines - all of whom are heavily armed against Wraith who are sick and dying. Sheppard's solution? Suffocate the hundreds of Wraith in their pods and use c4 to blow up any pods that are unresponsive to the "suffocate their occupants" command. When we don't have a clear answer as to "whose actions are more amoral, the heroes or Todd?" there's a bit of a problem
Designated Villain: Bates, Kavanaugh and Ellis tend to end up in this role. They usually have legitimate concerns or complaints, but because these are against the main cast of characters (Bates seeing Teyla as a security risk, Kavanaugh complaining to Weir about Weir dismissing his concerns, Ellis wanting McKay to cut the exposition and get to the point) the characters are presented as reactionary jerkasses. There is also a trend of portraying Kavanaugh, in his few appearances, as a coward even though every time he is up against a situation in which his fear is perfectly understandable.
Ellis isn't so much a Designated Villain as a Jerk Ass who likes to bully and harass those who make him feel inferior. He's a good man and takes pride in making the right call, but doesn't like it when people who are smarter than him have an idea or explanation that he finds difficult to grasp. Both times he doesn't tell McKay to cut the exposition and get to the point, he insults and harasses him for giving a long explanation, often one that is necessary to understand what he's trying to tell him. The first time, he cut him off and then McKay had to go back and explain the entire thing all over again because he didn't understand. The second time he outright bullies and degrades Rodney in a meeting so severely that Samantha Carter has to tell him that if he ever talks like that to someone again she'll have him forced off Atlantis. And that's really saying something (not that Sam is a mean person or anything, but she wouldn't defend Rodney like that unless what Ellis was saying was absolutely unacceptable, particularly considering that he's of equal rank).
Michael is a subject of some contention with this trope. Many people express their disapproval on how Michael is treated. It's easy to think that all this "Kill almost everybody and turn the rest into unstoppable army of destruction" kinda slips their mind. That said, disapproval of his treatment doesn't mean approval of his actions - just because the enemy is evil, it doesn't mean the heroes get a free pass to go play at the Moral Event Horizon. In a very straight use of this trope, though, some people do in fact sympathize entirely with Michael and do in fact forget that he ended up as an Omnicidal Maniac who would use a baby to perfect his mindless army, no matter what made him that way.
Engaging Chevrons: Played straight and subverted in "Rising". A big deal is made out of dialing the 8th chevron to actually get to Atlantis. Later, McKay slips into Walter's old "Chevron One... Encoded" routine the first time the Atlantis gate is dialed and gets a dirty look from Weir. After that it's never done again, since the Atlantis gate can be dialed in a matter of seconds.
Also Major Lorne and the gateroom tech. Fandom assigned first names to both of them (Evan or Nick — usually the former — for Lorne and Chuck Campbell for the tech), and the latter became a case of Sure, Why Not? and made it onto the show.
Todd the Wraith.
Fan-Preferred Couple: Depending on the fans preference for gay or straight couples; John/Rodney and John/Elizabeth. The former has a count of 2,516 entries on fanfiction and the latter 2,364. In comparision John/Teyla only has 1,184.
Fridge Horror: Sheppard's story in 'Remnants' when the characters control their own hallucinations. While Woolsey and Rodney create innocent and even happy visions of love interests and friends, Sheppard hallucinates Koyla taunting, beating and torturing him for hours on end. (Including cutting off his hand). And when he realizes it's not real? Turns out that he believes he deserves to suffer for everything he's done wrong. Worringly the series never returns to this so presumably Sheppard ended the series still drowning in self-loathing and emotionally torturing himself. (Made worse as all his friends have paired off and are living their Happily Ever After).
Genius Bonus: Genii is the plural form the Latin word "Genius" (no pun intended).
Growing the Beard: All the Badass characters either show up or are promoted in season 2: Ronon, Caldwell, Lorne, Sheppard, etc.
Sheppard and McKay are everyone's favorites with scenes that seems to back it up (the end of Irresistible for expamle).
Beckett and McKay are great friends and even kissed once while McKay was sharing a body with the mind of a female soldier.
A Foe Yay example is the relationship between John and Todd (the Wraith), especially when they formed the first human/Wraith alliance to escape a prison together. Though they're basically enemies and don't trust each other, they're friendly enough to work together in several episodes.
Ho Yay Shipping: Most notably, John Sheppard and Rodney McKay. There are some people who watch the show specifically because of this.
The entire retrovirus subplot in Season 2 & 3. First strike for carelessly leaving the unfinished formula out in the open for a scared little girl desperate for a cure to get ahold of. Then their experiment on a captured enemy Wraith backfires spectacularly and blows the expedition's cover. Then when aforementioned Wraith seems to put the incident behind him and offers himself as a potential ally, the team betrays him again. Unsurprisingly, it backfires just as badly as the first time, and they lose their own Hive ship for the effort.
Jerkass Woobie: The Asurans. The Lanteans tried to wipe them out, and the Atlantis Expedition later tries exactly the same because they're dangerous. Its even noted at one point that the reason they're envious of Humanity is because they see us as the favourite son who recieved all father's attention.
Of course, the "jerkass" part comes into play because their plan to destroy the Wraith was to wipe out their food source; in other words, every single human in the Pegasus Galaxy.
But this only happened because instead of rejoicing in creating artificial intelligence so advanced that it developed consciousness and compassion, and taking out the aggressive programming that made them a threat, the Altarens decided that they were Not Even Human and just wiped them out. After being treated like that its no wonder they are so distanced from biological intelligence: the only ones they knew were Abusive Parents.
The engineer in "The Ark" who was awakened to find that his family did not survive. He's completely distraught, and you sympathize with him. When he kills himself by burning himself up in the engines of the shuttle that was supposed to transport the last of his people, it's a little self-centered but still understandable... until you find out that he was trying to vent the entire moon station that he, his people, and the team were on into space via explosive decompression, using up all the fuel needed for the shuttle in the process of trying to kill himself and everyone else, and that in order to save these one thousand people he was complicit in the murder of hundreds of thousands who were slaughtered by atomic radiation in an Extinction Level Event that his people enacted so the project would succeed. Keeping in mind that this is the very last of his entire planet, and that the thousand left include two hundred children.
Magnificent Bastard: The Wraith "Todd" lives this as a matter of course; manipulating enemies with style is like breathing to him.
Major Sheppard also gets a moment like this every so often, including and especially at the end of the series, when he's trying to talk "Todd" into helping them fight another Wraith. "Todd" asks Sheppard why he should do it when it would leave "Todd" the prisoner of Atlantis and without any leverage.
Todd: Am I supposed to be enticed by this offer?
Sheppard: No. I'll probably kill you anyway. But don't forget, this Wraith betrayed you and got away with it. For no other reason, you might want to do it out of pure spite.
Todd: Youuuu know how to talk to me, John Sheppard! (evil laughter)
Moral Event Horizon: Kolya's feeding Sheppard to "Todd" the Wraith is seen as this by everyone, including Kolya himself.
McKay: Kolya! He could have left you to die! He does not deserve this!
Kolya: Let's be clear, Doctor McKay: no one does.
Turning Michael into a human for the second time, after he's not only sacrificed his own kind but helped the Atlanteans out multiple times, counts as this for some. The fact that the humans don't even think they're doing anything substantially wrong is what makes this even more horrifying.
Killing the Asurans comes close to crossing the horizon.
What Atlantis does to the Asurans who only wanted to Ascend - condemning them to an And I Must Scream fate - goes right over the horizon and keeps on going. Weir in particular stands out, as she was the leader of the group of Asurans and the betrayal is revealed to have been her plan, hence why went through the Gate first to convince them it was "safe" on the other side.
The Ancients attempt to wipe out the Asurans is equally horrifying. When we wished that the Ancients would have cleaned up after some of their messes, we didn't mean through carpet-bombing!
Nightmare Fuel: The hallucinations in the season 1 episode "Hot Zone", caused by an Ancient nano-virus.
In "Doppleganger", the malevolent crystal entity that assumes Sheppard's form in people's nightmares, is capable of scaring people to death such as Kate Heightmeyer and provides no real reason for it's actions other than It Amused Me. When it's returned to it's homeworld at the end of the episode, we see that there are hundreds more of these crystals stretching for miles around.
Shipping: A lot of it, with Teyla/Kanaan, Ronon/Amelia and McKay×Keller all now canon. (Although most fans were not happy about the last one).
As indicated above, the largest slash ship in the fandom is John Sheppard/Rodney McKay, although there is a decent portion that also enjoy seeing John/Ronon and Ronon/Rodney.
John/Elizabeth and John/Teyla were both Ship Teased. He has kissed both women at different times and have share quiet moments with them, but usually through some sort of plot device instead of actual romantic feelings. The Legacy series of spin-off novels still enjoy teasing the John/Teyla angle, but the novels' canonicity is dubious.
The John/Teyla ship was also neglected in later series as Ronon/Teyla was introduced and Kanaan/Teyla became canon. However the most popular straight pairing is still John/Elizabeth, especially as John remained single after her death (her death itself caused outrage among the fans).
The writers also Ship Teased Ronon/Keller before deciding to go the McKay/Keller route, which the fandom reacted much more positively to (it didn't interfere with shipping McKay/Sheppard, and Ronon was pretty popular so fans liked the idea of him getting to be with someone).
Strawman Has a Point: Michael points out the considering the Atlantis expedition's treatment of not only him but anything that isn't human or is a threat, they are incredibly similar to the Wraith. The fact is, he's right. If the Atlantis expedition had been the bad guys, their behavior would have put them beyond the Moral Event Horizon.
However, John's 'alliance' with Todd went a long way to helping to get back to moral ground, showing that yes, Michael was right, but being incredibly similar to the Wraith isn't always a bad thing. Remember, the only thing the Wraith can feed on is humans. They aren't the Goa'uld.
Furthermore, as several Wraith characters point out, it's not as if they have a choice in feeding. While they do possess a digestive tract and are capable of eating regular food, they lose the ability to gain any nutrients or sustenance from it during adolescence, when their need to feed on humans first manifests. Ultimately, the Wraith are just as much victims of their own biology, as the humans they prey upon.
He gets sent back to the planet after the people are immune to his charms. The implication is that he'll be plenty punished by the outraged villagers he manipulated.
We do find out later in "Irresponsible" that his wives divorced him and he was banished from the village, but even so, he seems to have been let off the hook rather easily. Furthermore, he doesn't appear to have learned a thing about why it's wrong to manipulate people, since he's right back at it in the latter episode!
Villain Decay: The Wraith seem to go through this, especially in the last couple of seasons, due to both Lowered Monster Difficulty and the story changing the emphasis from "the Wraith slowly wiping out all Pegasus humans" to battles against Eviler than Thou enemies such as the Replicators and Michael.
Todd also helped with the Villain Decay, because he gave a lot of insight into Wraith culture, and someone decided not to make them as evil as we were first led to believe.
Visual Effects of Awesome: Considering the typical production values of an average sci-fi TV series, the series has amazing CGI effects. Most prominent in "The Siege" three-parter episode.