If picking an item up before you are supposed to during your adventures breaks quite a few quests, than make those objects non-interactive until the proper quest phase is active.
From just reading the forums, most of the bugs are related to an item as such.
The other major bug that I have seen during my own experience in Skyrim, would be changing out NPC's in the cities depending on who has taken over (aka stormcloaks or imperials).
There are many quest turn ins that are broken right now for many people, because they helped either the imperials or the revoulution take over a city. Just doing this removes certain npc's needed for completing a quest.
The simple solution for this, would be to change the allegiance of the npc's that are NEEDED for turning in quests.
If not that, than simply replace the npc with one whom you can turn the quest into based on who has taken over the city.
Thanks for reading,
I hope Bethesda takes a look.