allcommands.com used to be free; now it's a brief free sample to
sell their book.  There are several books competing for the role
of everyone's favorite reference.  And there's linuxdoc.  And Google.
There is no standard, free, included reference.  RedHat might have 
the resources to have a better help system.

The big problem is maintenance and feature drift: maintaining
a reference to a thousand moving targets is not practical, so the
reference issue is decentralized with each package responsible for
its own documentation.

http://www.tldp.org/HOWTO/HOWTO-INDEX/howtos.html is a good starting 
point; it is organized by things you might want to do rather than
by smaller pieces.

The other big problem is what to include.  *nix is a framework, not
a closed set of tools.

Enough.