Absolutely agree... and the program will do the tagging for you. Just save, and all the external data, images, what have you... will now have a meta tag with the documents name. Rather simple.
I use a QuickLook plugin called SneekPeak for use with Illustrator and FreeHand files. When QLing the Illustrator files, it shows me which colors, fonts, and images I've used.
Take that one step further, and allow it to be an overlay window, and possible "Collect for output..Export...Sharing..." whatever, and the "Project Folder" necessity goes away.
Because I've been a rather prolific designer for some 30 years, I've always had to manage my hard drives, and try to keep duplicates to a minimum. I've generally used aliases for this in Project folders where I may use the same image from somewhere else on the HD.
Automatic quasi-"aliases" in metadata form would be far more useful.
Also, there were some people here pretending to be "pros" and why a file structure was necessary, and how they lose files because of being misnamed, etc. Do those people know how to use search at all?
And Gazoobee is not the only one that has seen desktops scattered. In fact, for the majority of people that I know, almost everything lives on the desktop: folders, program aliases, downloads... everything. In fact, if it's somewhere else, many people think they have lost it some how, and don't know how to find it.
One last observation. For all of the people here screaming how they want to use their computer or iDevice "their way", and demanding "Folder Freedom" and true OS X on the iPad, why do I think that they don't even have the slightest idea how to use OS X on a Mac right now?
For example, do you know how to use "Smart Folders", Saved searches, etc.?
What if "Smart Folders" became unobtrusive and an underlying feature on the iPad?