As I traverse the lands of Skyrim I'm constantly discovering new caves/mines and such...I absolutely refuse to fast travel unless it's mandatory for a quest. The only problem is that 99% of the time I will not go into them...I fear that they might be linked to some quest and do not want to disrupt a possible quest related Item or NPC.

Am I being paranoid about this or should I just charge right in and explore away?

Or create a list of caves/mines/ruins that should not be disturbed until quest is triggered.

I've wondered that myself....

If you clear a cave and need it for a quest, it respawns (atleast it has for me on the 360)

Almost all quest-related NPCs are essential.

Things will respawn for quests, but very occasionally there are quest items for quests that you haven't received yet. Picking them up can make the quests unable to be completed in some instances, especially if you're on the 360/PS3 (where console commands can't help you). An example is the quest in the mage college to pick up the book Chronicles of Nchuleft. I found it randomly in a dungeon/cave, but when I got the quest later, having it in my inventory didn't update the quest. I wouldn't consider this enough of an issue to avoid exploring though.

That's exactly what I'm afraid of...thanks for the heads up on that cave/dungeon...I have this quest queued in my journal.

Any other dungeons/caves/mines to be wary of this?

I will need to be careful since I'm on 360 and no convenience of 'console' commands....hmmmm *ponders' getting a pc for 'skyrim'

I suppose being wary is justified, but I've only had this glitch happen to me once. I picked up "Finn's Lute" in a dungeon I was clearing. When I finally picked up the quest to find the lute, I could finish it, but the 4 weight Lute wouldn't leave my inventory.

Annoying as that was, it was once in probably dozens of dungeons that I have cleared, onto to return later for another quest.

That's a long way of saying its probably not worth worrying about. Go dungeon diving.

Also, the radiant quest system will help you here, if you clear "Random cave X" and it would have been for a quest, instead it will send you to "random cave Y".