I also like the idea of making characters carefully chart what, and how, they're carrying. Like the OP, I've also found that this works better in theory than in practice.
I do like the "one piece of paper per piece of equipment" idea, but I wonder how well that'll work when you apply it to each one of a character's twenty-seven arrows.
So, now, I'm using index cards. Each card represents one piece of equipment. If a character loses his boots, then I take away that card. If a dagger is lost in a fight, then I take away that card. If a player gives his PC's favorite necklace to another, the card is transplanted from one PC folder to the next.
which we had enchanted to work as a communal bag of holding.
Yep, not to do it.
That said, if I was going to I'd opt for the method with the least makework. I'd probably use Excel or an iphone app to track items. That way you can automatically figure out weight/encumbrance, and it's easy to deduct for each day's food.
3e bags of holding are, I believe, pierced and ruined by unsheathed sharp objects; they don't have the catastrophic dimension-rending effects of earlier editions, though.
"How do you manage the bookkeeping without bogging down the game?"
Do you have a good system for tracking and placing equipment?
Can't share too much more without giving my own away, but tying in a large number of factors in a single stat isn't that hard (or uncommon).
However, as was mentioned earlier in the thread this kind of thing typically only comes up in early sessions at low level.
Umm, why not reveal your technique? Is there something I'm missing that requires you to keep it secret?