Spelunking for the 21st Century
QEMU is a generic and open source machine emulator and virtualizer.
The Elements of Computing Systems
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.
The OR1200 is an open-source synthesizable CPU.
What Every Programmer Should Know about Computer Memory
7-part series by Ulrich Drepper.