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.
Crazy Awesome: Rufus continually does things that other people tell him are impossible and/or will kill him. Despite all odds, his recklessness and arrogance lead him to victory time after time... albeit with a lot of collateral damage. It's even lampshaded in the third game, where people explicitly turn to him for a Crazy Enough to Work last-second gambit.
Dude, Not Funny!: See Darker and Edgier. In particular, killing the baby dolphins to make cat food can cause this reaction, as can feeding little orphan children to a monster.
The "organ grinder monkey" portion in Goodbye Deponia, so much so that it poisoned the rest of the game for many players.
Fridge Logic: You don't think much of it at the time, but upon further reflection the whole subplot with Goaly actually being an infant Donna makes no sense. Why did she have a radically different hair colour as a baby? The purple hair apparently isn't dye, since her hair turns back to that colour when Rufus gives her the nucleic acid. And how did Donna's corpse wind up with Goal's hair colour? Hermes has no reason to change it and Argus didn't know that Rufus had been thrown back to the surface (and survived), so it couldn't be him setting a trap either.
Harsher in Hindsight: Of all things, the tutorial level. In the first two games, it was an amusing hypothetical scenario where the player learns the basics and Rufus ending up getting squished by the junk press. In the third game, however, Rufus speaks of the room as a recurring nightmare of his during the tutorial session, which still ends the same way. But, halfway through the game, Rufus ends up in this room once more, and not only can he actually be killed, this time the player sees his bloody remains. Even though he revives after death, this cycle will continue until the player can figure a way out. After doing so, it's revealed that the press is part of the cloning facility where Rufus was made, and is used to process materials to make new clones from biomass.
Inferred Holocaust: The game ends with the original problem unsolved: Elysium needs to blow up Deponia so it can get to an inhabitable planet because it wasn't designed to stay in the air indefinitely and its resources are limited, otherwise it will crash into Deponia. Only now Goal and a good portion of the supporting cast are stuck on board, and they are going to need food, and the only remaining shuttlecraft was destroyed, meaning they are all stranded. Rufus is dead, and he was probably the only one who could think up a Crazy Enough to Work plan to fix everything, leaving only Cletus, which as the game points out is not Rufus even if they are genetically identical. Plus the entire Organon is also on board, and Argus might still be alive, and there's no indication he still won't carry out his coup.
Painful Rhyme: Every one of the narrator's intro songs is a stumbling mess of lyrics. The page quote is one of the few times he rhymes.
In the first game, Rufus ejecting Goal's brain implant and subsequently revealing to her that he's not really Cletus as they're ascending to Elysium.
In the second game, Rufus pleading with Lady Goal when she betrays him as well as Cletus giving him a Breaking Speech while he clings to a ledge.
Rufus believing himself to have killed Goal in the third game. Not to mention the whole ending.
The Woobie: Poor Bozo. He gets dragged into problems by Rufus, who makes fun of him all the time, calls him a pirate despite his insistence otherwise, makes free use of his ship, destroys his things, and eventually destroys his ship. And Bozo is too nice to do anything about it. Plus his girlfriend is violent and his family are kind of jerks.