I'm probably not the first to note it but it seems new tools for organizing knowledge are moving from directories-based (i.e. trees) into flat tag-based. We know that ubercool applications such as del.icio.us, citeULike, flickr use tags, but i realized today that even gmail does not allow you to create folders (and (sub)*forders) for your email messages but only to tag them. In this way emails remain in a single big pool but you can have different views over them based on the different tags you used.
I'm wondering if (and how) filesystems can move in a similar direction, or at least the "explorer" visual interface of a filesystem. VennFS (snapshot) seems an interesting direction even if I'm not sure the representation metaphor is easy to grasp. It is selfevident that the fact many people are used to directories-based structures does not mean this is the best way to organize knowledge.
A quick search resulted in 2 keywords related to tag-based system you may want to analyze more: folksonomy and ethnoclassification.
Pros of tags-based tools: an object can fall under more than one categories, you don't have to think once forever your categorization structure and then be stucked with it but tags support evolution.
Cons of tags-based tools: unless the tool incentives re-use of tags, you can easily end up creating too many tags and forgetting about them, resulting in inability to find the information you previously categorized.