Links

UNIX, Linux, and Scripting

    PuTTY - A free ssh client
    SFTP - The Secure File Transfer Protocol
 UNIX Tutorial for Beginners
 Dartmouth Shell Scripting Class
 Oklahoma State University UNIX Labs
 Links to lots of UNIX tutorials
 Knoppix a Linux Live CD/DVD
 Knoppix Wiki
    BCCD - the Bootable Cluster CD
    BCCD Wiki

Introduction and Computer Organization Links

 Operating Systems Introduction
 XSEDE - the Extreme Science and Engineering Discovery Environment
 cnx.org has a module on computer organization.
 Module on Computer Organization by Nguyen Thi Hoang Lan
 Wikipedia article on the Von Neumann architecture

Processes

 UNIX Processes
 Process States
 Wikipedia has decent articles on Processes and  Process Control Blocks
 Java Runtime Class
 C Pipe, Fork, Exec and Related Topics by Wolf Holzmann

Interprocess Communication and Message Passing Interface

 Interprocess Communication
 UNIX Interprocess Communication
 Message Passing Interface
 LLNL MPI Tutorial
 Introduction to Parallel Programming and Cluster Computing
 TACC Course Materials
 Purdue Tutorials
    Stampede User Guide

Threads

    POSIX Threads
    Multi-threaded Programming with POSIX Threads
 Concurrency in Java
 IBM Tutorial on Java Threads
 Thread Pools and Work Queues
 The Secret of Java Thread Pools

Synchronization

 Race Conditions
 Mutual Exclusion
 Semaphores
 Critical Sections
 Producer-Consumer Problem
 Producer-Consumer Demonstrations
 Readers-Writers Solution
 Readers-Writers Problem
 Readers-Writers and Monitors
 Java Monitors
 Dining Philosophers
 Deadlock Conditions
 Deadlock walkthrough
 Deadlock Prevention
 Banker's Algorithm
 Banker's Algorithm Examples

C Programming

 cprogramming.com
 Compiling with gcc
 C Programming  by Steve Holmes

Scheduling

 Wikipedia article on CPU Scheduling
 More on CPU Scheduling
 Context Switching
 Batch Processing
   

File Systems, Memory, and Paging

 File Systems  by Wikipedia
 UNIX File System article by Wikipedia
 NTFS article by Wikipedia
 Ext4 file system article by Wikipedia
 Paging article by Wikipedia
 Virtual Memory article by Wikipedia
 Shared Memory article by Wikipedia