Hear, hear. Since forever, I've used my ~ folder as pretty much my whole document base, and use search tools to sift through the contents.

I add simply ontology when specific tools require their own unpolluted namespace (ie, pine/mail) or need to be installed for multiple users (local box binaries).

iOS devices (as an example) just take this to the next level. In fact, I don't even use the main screen for launching many apps, I just type in the search screen to get it. If I could speak it in a seamless way, I'd do that instead.