The suceess of desktop search tools will probably signal an end to the way data is organized on the disk. After installing google desktop search i found accessing my files through desktop search was way easier than windows explorer. Explorer like interface is probably on its way out, i guess we will see file systems in the future which automatically store the data in a more logical way based on the contents, and freeing up the users from managing their data in seperate folders.
If i were to implement such a file system (in linux), i would provide a single folder where the user can copy all thier files. Whenever a new file is copied, it is indexed and all related files are probably clustered, so for example a user request for a listing of files (ls) containg a word (say simulated annealing) will be witten as "ls simulated annealing" and the fs should provide all files with the seachword in them. It can also list all files with some related words too (ofcourse with a lower priority). Would also be nice if the command "acroread simulated annealing" will open all pdf files contaning the word simulated annealing in them.