Linux/shell
Absolute basics
UNIX Tutorial for Beginners (Michael Stonebank)
Learning the Shell (William Shotts)
Intermediate, Shell Programming
Introduction to Linux: A Hands on Guide (Machtelt Garrels)
Linux Shell Scripting Tutorial -- A Beginner's handbook
References/Cheat Sheet
All the Best Linux Cheat Sheets
Linux BASH command line MAN page
Database/SQL
Beginning SQL by Paul Wilton, John Colby
It's an OK beginner book, there are nice examples throughout the book (lots of printout codes and results).
Comparison of different SQL implementations
A nice comparison of the different syntax, behavior of the SQL commands in different platforms.
Python
Python Programming for the absolute beginner
Dive into Python: Python from novice to pro
Perl
Comprehensive Perl Archive Network (CPAN)
Beginning Perl for Bioinformatics
R
The Comprehensive R Archive Network (CRAN)
Scientific Writing and Presentation
The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid
The Elements of Style (William Strunk, Jr.)
Scientific Writing and Communication: Papers, Proposals, and Presentations
Online resources
NIH traning series, many good presentations about career development and general matters in academics.
Complied by Joe Felsenstein at UW. A very comprehensive collection for online phylogeny analysis program/packages.
An Alphabetic List of Genetic Analysis Software
A very comprehensive collection for online phylogeny analysis program/packages. It's brief history can be found on their website.
A free informative directory for next-generation sequencing (NGS) and microarray data analysis.
Broad/Illumina Genome Analyzer Boot Camp
An online course for all the basic information you should know (and more) for Illumina seuqencing.
