yeah, it's one of those things that seems cool and a natural metaphor for the web, but in reality, at least until we get to matrix standards, just ain't going to be viable.
it's a bit like the 'desktop' metaphor, I saw a blog a while ago where someone was complaining about calling it a desktop because it wasn't that literal. I think that's silly, you adapt a system for the medium, not the other way round, and I think a 3d system, something that mirrors a process based on movement in real life needs to be adapted to work on the web, not somehow shoehorned into it.
a gallery was always the classic 3d environment people tried to translate to online, mirroring the process of walking through a gallery viewing images. Sounds cool but in reality it's easy to not have to 'walk' anywhere and just pick the images to view from a menu system. Creating something like this online allows you to devise a more user friendly system than actually having to walk around a museum, instead the online version is you enter the gallery, sit down and people bring you pics to look at!
Funnily enough, my dissertation is about the failings of the desktop/window metaphor
Basically, my view is that the metaphor is broken because it's so mixed; and also it's just unnecessary.
After all, the point of a metaphor is familiarity, so having a 'folder' that opens into a 'window' is actually a completely obscure abstraction from the original metaphor.
As for being unnecessary, we've just recreated the real world digitally and in the process thrown out half the benefits of having a machine capable of processing any information you can chuck at it.
i.e. why should I have to create a hierarchical filing structure in the first place? why recreate the folders and files of the real world?
My computer is easily powerful enough to manage my filing for me after all...