Vimal Joseph writes:
How to think like a computer scientist (python version) http://www.ibiblio.org/obp/thinkCS/
GTK+/Gnome Application Development by Havoc Pennington http://developer.gnome.org/doc/GGAD/
Just a word of caution. Many free software packages undergo rapid changes, for example Python and GTK+. If we were to print the manuals and tutorials related to these software packages, the printed book will become outdated soon. Yet another thing is that many people will not be willing to buy books for software packages that undergo rapid changes.
Vijay