Just to chime back in... I'm not looking for a "PERFECT" solution (well maybe I am, but I also know there isn't one... heh) but MAINLY I don't want to be 100% tied down to lightroom forever. Tags and such get into the files - that's fine, but a lot of it is proprietary and if I stop using lightroom I instantly undo LOTS of organization... at least with folders I have a (fairly) solid base to work off.
Having a somewhat organized folder structure also allows me to do something like fire up picasa and VERY QUICKLY browse through photos and such..