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This is the most important question treated here. To learn the basics about Gaussian input and output, refer to the "Gaussian 09 User's Reference". For templates, and to get many examples, check out/opt/gaussian/g09/bsd/examples.
There is a Gaussian web page with lots of information: http://www.gaussian.comThere is also a Gaussian user group that has many members who really know what they are talking about (and some who don't). Gaussian also operates a help line for licensed users. Send email to firstname.lastname@example.org , but don't expect the answer to come too quick, they get a lot of requests.
For hardcore computational chemists, there is the "Gaussian 09 Programmer's Reference" and the IOPs Reference which are useful if you want to tinker with default settings and internal parameters, or even want to write some subroutines of your own.
If you want to learn about the methods, check out "Exploring Chemistry with Electronic Structure Methods" by J. B. Foresman and Aeleen Frisch, Gaussian Inc. Pittsburgh PA. (This book makes reference to Gaussian 98, but almost all of it applies to Gaussian 03).
You can also ask Hartmut Schmider about specific technical problems with Gaussian. I am a theoretical chemist by training and have some background in the usage of the program.