As part of this manual, I would like to inculde a list of commands
that one would run to troubleshoot the LINUX machine?

Since I am also new to this? I would like some suggestions on the list
of commands I should include?

I am looking for commands which would run as a normal user and also
commands that would only run as root?

Why would you undertake such a task if you are new and lacking in knowledge
about such things? You have so much yet to learn about the system itself,
much more any troubleshooting of it, that I'm afraid to suggest that you
don't know what you've gotten yourself into.

Troubleshooting is an art as much as a science, and involves knowing how
things *should* be, as well as a firm grasp of how they *are*. The art comes
in deciding what tactics will be useful to gather evidence (which I gather
is your request here), and far more in interpreting that gathered evidence
to come to a tentative conclusion of the nature of the problem.

How one explores a problem has everything to do with the nature of the
problem, but how one interprets the results is even more important. You can
make a list of diagnostic commands such as ls, find, df, du, groups, strace,
top, echo, traceroute, ping, netstat, umask,and many, many others, but the
data returned from any of them will only have utility in certain situations.

If a person is new to *nix, probably the best diagnostic command they can
learn, and learn well, is "man". Then they should spend as much time as
possible at a site such as http://www.geek-girl.com/Unixhelp/ and get to
know it inside-out and upside-down.

Then they'll be able to understand the way things *should* be, and they'll
(hopefully) be able to see their own contribution to their problems rather
than blaming everything on the machine.

Most problems are between the chair and the keyboard.

          tony

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I agree.  Its like saying you've agreed to write a manual for
troubleshooting cars and what tools do you need to fix and diagnose them.
Each response will warrant its own tool or set of tools.

While most would love to help you with this endevour, the best is to use
"man" as mentioned above.  Also, google searches will help enormously.  My
strongest suggestion is to purchase a few Linux books from a store and use
online resources vs compiling a guide that may prove to be useless.

ken k