Update 2010: Please see the docs.google.com edition of the guide as it has the latest material. See link below.
There is a new guide on how to write Greek and Greek Polytonic in Linux, and in particular using the latest versions of Linux distributions.
https://docs.google.com/View?docID=dccdrjqk_4cqjn9zcj (LATEST VERSION)
The guide shows in detail how to add the Greek keyboard layout to your Linux desktop, and how to write Greek, Greek Polytonic and other Ancient Greek characters.
The guide is also available in both ODT and PDF format. (both files are somewhat obsolete. use google docs URL from above instead)
For a Greek version of the guide, please see http://docs.google.com/Doc?id=dccdrjqk_3gx3bq5f9 (does not update as often as the English version)
We attach the HTML version of the guide in this post. The docs.google.com version is the latest, please read that instead.