> To your question though, the VN-specific jokes are mostly about the route system and world building. I guess these still fall under the umbrella of "bad endings" and "save then go back" but imo it's a huge umbrella that's worth exploring.
I'd also include the (sometimes literally) faceless protagonists in this. For the uninitiated, it's a fairly common trope in romance VNs that the face of the protagonist is obscured, supposedly to let the player self-insert. In DDLC, if I recall correctly, you mostly see the protagonist's hands and in one image his back.
This trope leads to some fairly weird looking haircuts or (more commonly) to graphics where protagonists simply have no eyes. Perhaps fittingly, this also sometimes applies to characters that are so unimportant that they get labels such as "Student A" instead of proper names, if they even get sprites at all.
DDLC takes it to the logical conclusion that it is the player that matters, not the paper-thin player stand-in