Maybe quests like "mercenaries for sohaty" and "owl of wisdom" rank up there because they depend on certain items or units being available to buy.

I suppose but those two are ones I definitely do not miss. The owl one is particularly painful because I spend the time for the extra trip. So that makes three (burial is the third) that folks consider frequently missed but is not the one I almost always miss. Hum. Is the name of all completed quests stored on disk? Is it easy for me to extract so I can form a sorted list to compare with other games ?

You can see all quests here:
Armored Princess WALKTHROUGH

not everyone wants to play exactly as in walkthrough thats why people miss quests in their first play.On second play i always check walkthrough to get most of the game. :) So the link is usefull to us all :)