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.
The mere fact that in the Black Market, one of the merchants is a plant!
In fairness, it seems to be implied that they're a normal person, just disguising themselves as a plant for some reason. It's still comically absurd, though.
Alicia's snarky commentary if you profess love to Marie.
Marie: Of course I want you to here with me, for as long as it takes! Maybe even...forever... -romantic music abruptly cuts out- Alicia: That...is...ADORABLE! Marie: Wh-What?! Hey! Hello, private conversation going on here! Alicia: I'm pretty sure the entire room heard you. FOREVER! That is just...too much, Marisol. Too much.
Superstar: Obtain all other merits. Also, go outside.
The resolution of Chac's sidequest, in which Sorenson himself helps pull Chac back from the Despair Event Horizon.
At the resolution of Soran's sidequest, if you are inquisitive enough, you can learn what he's using all that carboderm for. He wants to seal himself in a ball of the stuff until society's rebuilt and everything returns to normal — he doesn't care how long. Effectively, it's suicide. If you are persuasive enough, you can talk him out of it and convince him he has a purpose in life.
All of your crewmates banding together and defending you from Thomas' verbal assaults in episode 4, each of them creating an on-the-spot Rousing Speech.
The parts of the optimist ending that aren't Tear Jerker are this.
Crowning Music of Awesome: Space Lizard is making a completely unique soundtrack this time around, and some themes are pretty catchy. Of note:
"All Good Things" is a reference to the proverb "all good things must come to pass", which probably refers to the Back Story of the Shine destroying almost all of humanity's accomplishments.
"Castles of Sand" is also a reference to a proverb, with the meaning of a fortress that seems secure, but is actually worthless and easily infiltrated/destroyed. Since episode 1 revolves around defending and rebuilding, that's pretty ominous.
"His Master's Voice" was the slogan of a recording company, who claimed that their recording technology was so authentic that a dog would not be able to differentiate between the record and its master ... and in The Reconstruction, we have a group of "Watchers" who claim to take orders from "The Voice Himself". Possible Foreshadowing?
Typelog also records information, so it could be referencing that.
"And Yet It Moves" are the words that Galileo (supposedly) muttered under his breath at his trial after being forced to recant the Copernican theory. Episode 3 revolves around EROS, a secretive group whose views clash with those of Typelog. Most likely, the famous phrase is meant to draw a parallel to their conflict with Typelog — conforming to the unquestionable views of authority versus freedom and a lack of limitations on science.
"Forever And Ever" is a common phrase in The Bible, usually referring to God or the heavens. Mostly, it seems to be be an ironic counterpoise to a major theme introduced in episode 4, which is that nothing lasts forever or is truly infinite.
"A Plan For Everything" is also a religious reference — God is often said to have planned out the destinies of all aspects of the world in advance. This probably refers to the Progenitor's wish to invoke this by creating a god that has the power to plan and direct everything towards harmony in the new universe.
Ivoronus' final transmission to Mahk as the Machinatorium is destroyed.
Everything surrounding Mahk in episode 5, really. Especially since he dies in The Reconstruction, so they last the crew ever sees of him is him having a nervous breakdown and running off to find Tezkhra...
That One Sidequest: One sidequest requires you to accumulate five hundred thousand half-credits. And not just the total amount of money you've gotten over the course of the game, either — you need 500,000 credits in the bank.
What an Idiot: Both characteristically and uncharacteristically for Tezkhra, he admits in one side conversation that he deletes his Typelog files if he doesn't think they're necessary, to maintain order and conserve space. How he didn't think this would come back to bite him is beyond us. Probably it's an excuse he made up himself though, and the real reason was crucial information about his identity no one should know about, including himself.