When you finish the game and have the choice to start a fresh or continued game, if you refuse 3 times it starts a new game anyway, except you hear a demon laughing and your title becomes "sacrifice of the abyss." It's creepy.
For some reason when your karma is 100, you can understand what the cow is saying when you return to Misthorn (It's just about how her milk has been squeezed dry... *shrug*)
The Coldia minister has a porn book in his bookshelves, and there's even a hint about it in the "Citizen's" apartment room, but it wasn't even possible for the player to reach it. I think the author didn't realize the flags act as barriers, so I moved it to a reachable location. There's an unreachable fairy coin in the ruins before Endoll castle that drives my OCD nuts too.
There's a Fran's Dream #2 in both the CG room and in the event scripts, but they're empty.
There's a bug in the yariel's version where if you do a new game plus the farmer in Misthorn would give you milk for the quest again and again but the quest wasn't possible to complete. I restored it to the original game's scripts to fix the bug.
As far as I know there's only 3 story-based karma checkpoints. If your karma is 0 when the pirate ship sinks, or when you stay the night at the Ceres monastery, you get extra dream scenes of Fran's past. One of them has books with scattered text that are a pain in the butt to translate so I don't blame yariel for skipping it. Maybe I will make an attempt later. There's the sword in the Oldelion temple but actually that has no relevancy to the story.
The last checkpoint that decides the endings is when your grandpa dies. If you didn't read the book in Fran's house after defeating the Barbatos family in Endoll, you get the normal ending. If you read the book and your karma is 50 or higher when your grandfather dies, you get the 'bad end'. If it's lower than 50, you get the 'true end'. (Once you reach 50 karma in the game you can't reduce it lower than that, afaik.)
I think there's plenty more but that's all I can remember for now.