Languages

C

• The C book
• The new C standard – an annotated reference

C++

• Thinking in C++
• C++ Annotations
• How to Think Like a Computer Scientist
• Software optimization resources by Agner Fog
• Effective STL by Scott Meyers
• More Effective C++ by Scott Meyers

C#

• .NET Book Zero: What the C or C++ Programmer Needs to Know About C# and the .NET Framework
• Data Structures and Algorithms with Object-Oriented Design Patterns in C#
• Threading in C#

Common Lisp

• Practical Common Lisp
• On Lisp

Haskell

• Real world Haskell
• Learn You a Haskell for Great Good!

Java

• Thinking in Java
• How to Think Like a Computer Scientist
• Java Thin-Client Programming
• OSGi in Practice (CreativeCommons Attribution Non-commercial Share Alike License)

JavaScript

• Eloquent JavaScript
• jQuery Fundamentals (starts with JS basics)

Lua

• Programming In Lua (for v5 but still largely relevant)

NoSQL

• CouchDB: The Definitive Guide

Objective-C

• The Objective-C Programming Language

Perl

Perl 5

• Beginning Perl
• Extreme Perl (license not specified – home page is saying "freely available")
• Embedding Perl in HTML with Mason (Open Publication License)
• Practical mod_perl (CreativeCommons Attribution Share-Alike License)
• Higher-Order Perl
• Learning Perl the Hard Way
• Perl & LWP
• Perl for the Web
• Web Client Programming with Perl
• Modern Perl 5 (Work in progress)

Perl 6

• Perl 6 (Work in progress)

PHP

• Practical PHP Programming
• Zend Framework: Survive the Deep End

Prolog

• Building Expert Systems in Prolog
• Adventure in Prolog
• Prolog Programming A First Course
• Logic, Programming and Prolog (2ed)
• Introduction to Prolog for Mathematicians
• Learn Prolog Now!
• Natural Language Processing Techniques in Prolog

Python

• Dive Into Python
• Dive Into Python 3
• How to Think Like a Computer Scientist
• A Byte of Python
• Python for Fun
• Invent Your Own Computer Games With Python
• Thinking in Python

Ruby

• Why's (Poignant) Guide to Ruby
• Programming Ruby – The Pragmatic Programmer's Guide
• Mr. Neighborly's Humble Little Ruby Book
• Ruby Best Practices
• MacRuby: The Definitive Guide

Scheme

• The Scheme Programming Language (Edition 4)

Shell

• Advanced Bash-Scripting Guide (An in-depth exploration of the art of shell scripting)
• Mastering PowerShell

SQL

• Practical PostgreSQL

x86 assembly

• Paul Carter's tutorial
• Software optimization resources by Agner Fog

Algorithms and Data Structures

• Algorithms
• Data Structures and Algorithms with Object-Oriented Design Patterns in Java
• Planning Algorithms

Frameworks/Projects

• The Django Book
• The Pylons Book
• Introduction to Design Patterns in C++ with Qt 4 (Open Publication License)
• Ruby on Rails Tutorial: Learn Rails By Example
• The Definitive Guide to symfony

Text Editors and IDE's

• A Byte of Vim

Version control

• The SVN Book
• Mercurial: The Definitive Guide
• Pro Git

Release Tools

• Maven by Example
• Maven: The Definitive Guide

Unix / Linux

• The Art of Unix Programming
• Linux Device Drivers, Third Edition
• Advanced Linux Programming

Others

• Structure and Interpretation of Computer Programs (Creative Commons Attribution-Noncommercial 3.0 Unported License.)
• The Little Book of Semaphores
• Mathematical Logic – an Introduction
• An Introduction to the Theory of Computation
• Developers Developers Developers Developers
• Linkers and loaders
• Beej's Guide to Network Programming
• Domain Driven Design Quickly – based on Eric Evans's book.
• Let's Build a Compiler, by Jack Crenshaw
• Producing Open Source Software
• How to Write Parallel Programs
• Don't Just Roll the Dice (A usefully short guide to software pricing)