This is a weird system/mechanics, but how the "quest log" system in Morrowind was implemented as its journal was perfect. I've always felt like that was the high water mark of "quest mark system", and no other game has thought to copy it and I never knew why:
1 - When something happened in game that caused the journal to update, and you go the notifier for it, the journal didn't just say "X happened", it would often have flavor text. It's written like it's by an actual person and not a yellow-text machine.
2 - The flavor text likewise acted as a soft hint instead of a hard "Do X" if you were stuck about where to go or that you might want to reload. It wouldn't say "Quest failed", it'd say "X wasn't happy with how you did..."
3 - The indexing system allowed you to not only jump between quests, but also had keywords carefully selected so you could figure out intersecting quests.
4 - Due to 3, something that I loved in Morrowind in general was the encouragement of research. I would hoard books, and then spends hours reading them all, cross-reference them against my journal's bookmarking index system, and figure out where hidden treasures and ancient ruins were. Sometimes you'd find in some tome warning you of a huge Dwemer mechanism, and you'd feel proud you didn't get ambushed by it because you have an IQ above your shoe size and can read. I loved how a return back to my home base involved figuring shit out and planning for the journey.
5 - Related to 3, modern quest logs will just @#$!ing DELETE old quests so you can't reference what you already did or had already been.
6 - How it was enmeshed: it wasn't a weird abstract HUD element that took you out of the experience, it was a journal that you the character actually held. When you flipped pages it made a sound that sounds like you flipping pages.
7 - Switching back to chronological. Sometimes I'd be reading through a quest log figuring something out, then think, "Wait...didn't something like that happen a week ago?" And I would flip back my journal a few days to review. Just--you know--like real life. Also helped when real life got hellish.