Is it possible to let Spotlight find files and directories from all over?
I'm not aware of a solution in Spotlight with(-out) tinkering.
It certainly would add a lot of "trouble" to users with HDD as the the amount of file to index will be too much - hey, after all it's the
Quicksilver allows to index user defined directories in Preferences → Catalog. You can then define the dept to which you want to descend. Optionally, you can even descend in bundles!
It may not be exactly what you're looking for, but you can access the backend database of Spotlight directly from the command line with the mdfind command.
mdfind blah will search nearly everything on your drive (not just the stuff Spotlight shows) that matches "blah" - in file names or indexed contents, like Spotlight. It's not a nice GUI interface, but for the occasional search for something Spotlight won't find, it's a good built-in option.
There's also Find Any File, which doesn't seem to use indexing, but rather does a full disk search, so expect it to be much slower, but not limited by Spotlight/mdfind's exclusions.