haligtree was easy since there's an NPC who tells you where to find the key. I had to google how to use the medallion, though. Was standing right in front of Rold Elevator not knowing what to do, because I didn't notice that you could switch between "hoist the normal medallion" and "hoist the secret medallion" prompts.
mohgwyn palace - stumbled upon the teleporter organically while exploring Consecrated snowfields. I actually completed the sidequest from the creepy dude who calls you maidenless before, and received an item that was supposed to teleport you to Mohg as a reward. However, 30 hrs later I completely forgot that I even have that item.
the Leyndell sewers proper
Leyndell sewers - just found it organically.
Three fingers sanctum - i thought it would be weird for Mohn The Omen to be the end of the dungeon, so i started rolling into walls to check for illusions.
Haven't been in Azula yet.
I've noticed that a lot of minidungeons and caves were hidden under cliffs, so I started to check edges of cliffs everywhere and found Jarburg.
figured out the entire Ranni's quest
didn't figure it in its entirety, skipped some beats, and in some cases progressed by accident. For example, I didn't know you could meet Blaidd in Mistwood.