Hi 0n1x, welcome to Planeshift!
Items that say "guarded by XYZ" are locked and you will not be able to pick them up. I personally believe it is OK to pick up anything else, unless you believe it is something of value that may belong to someone and should be returned. Then it's up to your character's alignment, a rogue or thief would certainly do away with them and have no qualms.
Being a thief now brings up this problem: How do you steal from someone if you can't get their items even if they put them down? In this case, just whisper to them that you are a rogue character and want to steal from them. It makes sense to /roll a dice and set a result above which you succeed. A number bellow which you get caught is also a fair deal. So say you /roll 20, you succeed above 15, get caught below 5. If they agree to your RP, then they will let you have what you steal.
As for the examples you ask about: I would pick up animal parts lying around unguarded, they are low value items and most probably were left there by someone who didn't care about them. Ores you find in mines on the other hand are ores that spawn there, sometimes even above ground, and they are yours to just pick up.
Migg