In my old Squirm, there was a quest which required you to catch a runaway pancake, which could be picked up. The code had Critters and Items as subclasses of the same mother class Being, so it wasn't too hard to code. If I recall correctly, I just put an "actor" flag on the pancake, while making sure it lived on the same layer of the dungeon floor as regular items, whereupon it started speeding around. Once in your inventory, it just sat still, but it shouldn't be too difficult to implement a system where stuff acts from within the inventory. Designing the system should prove more difficult, but it could be used for stuff like the Philosopher's stone (turns your other inventory to gold), uranium (slowly poisons the carrier), or leak bottles (ruins scrolls). Allowing for stuff other than actual critters to act can even be used for dungeon features that should have some sort of effect – altars boost morale of nearby followers, lava pits occasionally splash magma, that sort of thing.
And actually picking up other critters does certainly rule. Maybe Dungeonjacks has something like this – it's based on the board game Blood Bowl, where big monsters are allowed to pick up and throw smaller monsters.
As always,
Minotauros