So I've been wondering, when you use, say, a Sierra Madre Vending Machine, or give items to Muggy, or use benches. Where do the items GO? I mean, do they just get deactivated from the game, or do they go to some sort of 'netherworld' of sorts where unspawned items go? Sorry if this is random or weird, it's just a curiousity thats always been on my mind.

I think they are disabled upon them being removed from your inventory. Then again, I barely even know what a GECK is, so someone else may be of more help.

Yeah, thats why Im asking, because I'm curious about the games inner workings, but my PC isnt capable of running New Vegas.

They just remove them from the game. To send them off to some other netherworld would just add to the memory the system would require as it'd be forced to keep track of every item ever given to the vending machine or Muggy.

The above are how it works.

The Pip-Boy's inventory lists are basically a set of containers, although they don't have a GECK entry you can tinker with. As such, the items within do not actually exist save as a collection of RefID markers, so when you 'use' one the inventory script uses the 'removeitem' command to disable the appropriate number of copies of the RefID in question and delete it/them from game memory, and then increments the appropriate counter. When you drop one or more of an item, the game actually spawns the appropriate number of physical objects on the fly; since the objects themselves are persistent references they don't vanish when the cell resets, however if they're picked up the object de-spawns immediately and is replaced in the recipient's inventory by a RefID marker as above.