I don't think any game has a perfect inventory system, although some come close.
Ultima 7's inventory is pretty cool but the absence of information and item inspection really hurts it for me. In a game that sets out to create an alternate world, I don't see why each item wouldn't have its own description for you to read.
Apart from the aesthetics, each item has its own weight and size values (yes, even gold) but there's no way to tell what they are except by experimenting. Even though you might not realistically know exactly how much a sword weighs, or that two loaves of bread is equal in size to four apples or whatever, this information should be available to the player as it's something the character would be able to work out just by holding or looking at the items.
Underworld lets you go bagception as had been mentioned, but each bag & your backpack has a limit of 8 items.
Wizardry 8 had a nice party pool system where each character shares the burden, and it took an extra turn to 'retrieve' an item from this pool during combat. But each character had a limit of 8 items they could carry. Considering that the game took into account encumbrance and that the party inventory had a scrollbar, why was there this limitation?
King's Bounty, while not a proper RPG, had a grid based inventory that got larger as you picked up more items. Something other grid-inventory games could draw from. However it wouldn't let you have empty space between items which was a shame, although it did have sorting by type & value.
I think when it comes to comparing inventory systems it's important to break it down into the system (backend, how it'd work in P&P) and interface. Many games have systems limited by their interface, or other design limitations. At least that's the only reason I can think of for some of the limits in most old school games.
Then there's games with plain bad interfaces like Stonekeep. Would it have been that bad if you could open a full screen grid inventory, rather than the 'slick' 'streamlined' side scroll inventory? Same with Fallout & Daggerfall. The idea itself wasn't bad, just the interface and way you interacted with it made it unbearable.
Other games had importing & exporting of characters, which probably had design limitations on how many items characters could carry.
Most newer games have alright inventory systems in that they follow the 'limitless' inventory limited only by weight, but have absolutely horrendous interfaces to go with them. Whether it's items having no icons, or just icons for categories (Skyrim, DA2), or the icons themselves just not being unique enough (DA:O). The Witcher 2 from what I remember had decent icons but only displayed a handful of items at once (thanks XBOX!).
In terms of my perfect system I think my criteria would be
-Inventory limit only from encumbrance, and possibly item size
-Every item having a weight & size value, no matter how tiny
-Items represented with iconic icons in inventory (one of the things the IE games did very well IMO)
-Ability to manually move items around in a limitless grid, leaving spaces between them, but also view your inventory as a list allowing sorting (which wouldn't move your manually placed items)
-Descriptions for every item
Ultima 7 modified to display item weight & size, and have indications for how much more crap you can stuff into a bag would make me happy too, but this system doesn't suit every game.