DeepHack

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DeepHack: Spelunking for the 21st Century

QEMU

QEMU is a generic and open source machine emulator and virtualizer.

QEMU Secret Motor uses QEMU to create visualizations like this.

The Elements of Computing Systems

MMIX

MMIX is a 64-bit RISC machine used in Volume 4A of Donald Knuth's Art of Computer Programming and it will eventually be used in all other volumes of that series.

Open Computation Hardware

The OR1200 is an open-source synthesizable CPU.

What Every Programmer Should Know about Computer Memory

A 7-part series by Ulrich Drepper (complete PDF):

CorePy

CorePy: Assembly Programming from Python

Operating Systems

Systems-level software (kernel and userspace)

Unix V6

Linux

A Plumber's Wish List for Linux

Looking for a useful systems software project? Version 2 of the list by Kay Sievers (20 Oct 2011).

Linux 0.01

Minix 3

Roadmap including ARM support.