I think there is a correlation between interface style / tactile-ness and "toy vs. simulation". Where objects drop on the ground or appear in a pop-up list, comes too the feeling that the game is more a toy. Where creatures lie, waiting for their valuables to be rifled through, comes more of a sense that the game is more of a simulation.

Depending on how you want to present your game (toy vs. simulation) helps you choose how to present the interface to the user.

Personally, I prefer the simulation route.

This topic reminded me of probably one of the greatest game promo's ever, the Bling Gnome from Dungeon Runners.

The way it worked is any loot that dropped on the ground from an enemy or chest that was below a certain quality the gnome would digest and then...give you money for it as if you had sold it to an npc shop. Here's a link to the promo video, it still cracks me up!

Some games have capacity limits (slots or weight totals) where auto loot generally would be very bothersome.

Filters might be helpfuil but again that depends on how many kinds of loot and how complex the filter controls would be.