With regard to the actual system I tend to agree with DraQ, weight and size should both play a factor idealy, and seperate storage areas are a big plus. Ultima VII is quite a pretty solid example of my ideal system.
In terms of the actual inventory managment (GUI, sorting etc.), I think there'd be a lot to be learned from looking to file manager systems used by operating systems. Boring, I know, but it's a system that works and also a system you know most people will be familiar with (pc players at least). Some such elemets that could be transfered to an inventory system:
Changing views (list, icons, details)
Sort (by name, weight, value, time collected etc.)
Filters (weapons, armour etc.)
The ability to select multiple items (drag box, ctrl, shift)
Using storage bags like you'd use folders, with the ability to rename them (e.g. ingredients, weapons, loot, whatever).