The entire attempt to get onto the Organon Cruiser at the beginning, from the launch to landing.
Rufus mistaking Liebold for someone else. Gets funnier when you step through the time portal beforehand and get a mysterious dialogue with him.
The optional death scene in the second game, complete with old-school Sierra-style Restore/Restart/Quit screen.
In the prologue for Chaos on Deponia, Rufus sees a button with a dusty display that can change to one of three options that could save him when blown upon. After pressing it, however, nothing seems to happen, causing him to blow off the rest of the dust for answers. It turns out to be an "Eject Goal" button