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.
Complete Monster: Sirrus is a mass-murderer. As his brother Achenar felt remorse for his actions and does a Heel-Face Turn and Heroic Sacrifice in Myst IV: Revelation, Sirrus not only seems to have no regrets but commits additional atrocities: kidnapping his own sister, taunting her about how he plans to suck her soul out of her body before doing a Grand Theft Me, and then holding her soul captive if the player manages to get his soul out of her body. He taunts her about how he plans on murdering both her and their parents, and in the bad endings where the player loses, he murders his brother and the player.
Crowning Music of Awesome: Examples are few and far between, given the ambient nature of the games, but the one that stands out the most is "Curtains" from Myst IV, sung by none other than Peter Gabriel.
The main themes for Myst III and IV by Jack Wall are also pretty epic.
Jerkass Woobie: Saavedro's been through a lot of shit thanks to Sirrus and Achenar, and deserves the chance to finally go home, but he's still a gigantic dick about the whole thing; several of the bad endings have him smash your head in with a hammer in a rage. He will even do this if you fulfill all the conditions necessary to get the good ending, then open the door that has thus far kept him from getting at you up until this point; apparently he doesn't really care if you've kept your word or not, he just really wants you dead for being on Atrus' side.
For the other bad ending, comply with his demands without question and he'll just chuck the Releeshann book over the side, as if to say "Thanks for the help, oh, and if you see Atrus, tell him to kiss my ass!"
Kadish, too, in URU. He wrote many of the Ages the player visits, such as (obviously) Kadish Tolesa, Eder Gira/Kemo, Er'cana, and Ahnonay, but the lattermost is what really drives it home: its whole purpose was to make visitors think, through a series of rotating spheres, that he could make Linking Books warp to different times and spaces, something only the Grower, a mythological figure, could do. The final, unfinished dome contained an enormous statue of himself.
Moral Event Horizon - All pity for Sirrus drains away when you decode one of the conversations at the end of Myst IV. Hearing the way he's taunting his child sister about how he's going to suck out her brain and murder her parents is... well, it speaks for itself.
The intro actually has a too-fast-to-see frame of Gehn looking at you as a subliminal message to give you the feeling someone's watching.
There's a door on "Temple Island", where you start - it's locked, but you can crawl underneath it. What's behind it? Nothing, except a small peephole into the temple.
When the temple is rotated properly, the door gives access to the valve that powers the Star Fissure scope. The reason it's locked is that Gehn probably didn't want anyone else using the scope.
There's a throne room (of sorts) near the temple, connected to it by surveillance camera and holographic imager. If you enter the temple, sometimes the imager will be running and you can see Gehn hurriedly switch it off - and you can't catch him before he escapes.
During the normal course of events, the first thing you find is the transmitting room, which contains the holographic camera, and the two surveillance monitors which show the inside of the temple and the monorail terminal outside; there's also a switch to open and shut the temple's main door. The next thing you find, just down the corridor from the preceding room, is a secret entrance to the temple. The game permits you to put the full picture together yourself: Gehn is in the transmission room; he waits for representatives from the village to arrive via the monorail, at which point he flicks the switch to open the door, sits down in the throne, and lowers the hologram apparatus into position; his image is then projected into the temple to speak with his lowly subjects, who most assuredly have no idea that they could reach him simply by finding the door and walking down the hallway. He has a terrifying amount of technology invested in making the more superstitious of the villagers view him as omnipotent. This is by no means the only manifestation of his controlling nature, but as early glimpses go it's profoundly unsettling, and gives you a very good idea of whom you're up against.
There's a periscope in the middle of the lake on Village Island, which turns out to be connected to another hidden surveillance room. Fortunately, when you're out wandering around the lake, it's not used. However, Cyan originally intended to have the periscope pointed at you the entire time, but it was too complex to render in every shot.
Porting Disaster - Porting the original game to the Nintendo DS did not go so well, given the DS's lower resolution and lack of a context-sensitive mouse cursor.
It's worth noting that, other than very minor issues with the smaller screen, the port to the PSP is actually quite good.
The 3DS version isn't much better than the DS version. It uses a cursor at least, but it doesn't use the 3D functions, nor does it use the touch screen for anything important. What makes it worse is the blatant false advertising of the promotional materials, which claim that it displays in 3D, when it doesn't.
Player Punch - The final part of Sirrus' memory sequence on spire. We begin seeing Sirrus raging against his imprisonment, then deciding to escape and discovering he can't get down to where the linking book must be, and deciding maybe if he can get to another of the structures he can see, he might be able to climb down from there. We see Sirrus' working on a way to get across and beginning to wish so much he could show his father what he was achieving. We see him beginning to miss his family, and grow closer, and closer and closer to repentance, making images to remind him of happy times in his youth or thinking about what his family might be thinking or doing. Then we see him complete his efforts, get below the cloud layer, and discover the surface of a burning star that the stone structures of Spire float over that has obviously incinerated the linking book below. ...And then we see him snap.
The show of missing his family was an act to ingratiate himself to his mother, since it's all built within the survey of the viewer. His own journal entry reveals his motive.
"Perhaps if I play upon her guilt. Create a sculptural vignette which she can see inside their viewer. If I choose the appropriate memory, it should convince her that I, too, have my regrets."
There's also the moment in Riven where you read one of Gehn's journals. He's crying about his deceased wife, Keta, and unlike the neat and ordered previous pages, the pages on this one are stained with tears. The worst part is is that you have to trap him before you can learn about this.
Just in case you didn't know how much he misses her, there is also a photograph of her and a short video message where she promises always to love him "to the greatest extent".
Saavedro's journal in Myst III: Exile. It starts off as a straightforward journal about the details of his revenge, but as you collect pages for it (which are scattered around various ages), more of Saavedro's backstory forms - he's clearly suffering severe mental trauma from his ordeal, was essentially tortured by Sirrus and Achenar, and once trusted Atrus before his sons ruined everything. It's quite tragic to read the whole thing once you have all the pages.