Good resources to get started
Introduction to Linux
Unix and PERL for biologists (good for novice)
Unix Quick guide (good for novice)
Despite its (scary) name, this is an excellent no-nonsense tutorial! http://cli.learncodethehardway.org/book/
GNU Core utils for working with files
LinuxCommand website is good place to get started on some command-line-fu.
Programming:
Really good thoughts on programming language environments, learning, and thinking
Text editing in Linux:
Pico: For the beginner. Pretty simple and gets the job done
VI: your best, complicated friend for almost quickly editing text files:
The command 'vimtutor' that can be found on popular Linux Distros is a quick way to get acquainted with vi(m).
http://heather.cs.ucdavis.edu/~matloff/UnixAndC/Editors/ViIntro.html
Eclipse: When you want a full blown IDE
Programming for kids: (really neat way to start)
Linux Foo: http://www.linuxquestions.org/questions/linux-newbie-8/what-is-foo-468303/
tmux: (awesome virtual console manager)
Let's you keep a "screen" active while you are logged out of the system
screen: (level 1 virtual console manager)
Code Versioning:
GIT concepts simplified (from the ACM club's email): It covers a lot of git concepts and explains them all graphically.
Virtual and Cloud Computing:
Virtual Box: Virtual machines on your machine.
Amazon: EC2 (requires $$$)