Useful Links

Malware Anaysis

Zynamics - Halvar Flake and associates
nruns - Questioning the effectiveness of existing AV infrastructures
Art of Reverse Engineering - A large collection of unpacking and inline patching tutorials
Open Reverse Code Engineering - Reverse engineering blog

Virus Collections

0x29a - 29A Labs
VX Heavens - Lots of viruses
Offensive Computing - A nice collection of RE information and virus samples

Debuggers, Et Cetera

OllyDbg - 32-bit assembler level analysing debugger for Windows
Immunity Debugger - Powerful debugger for analysing malwre, writing sploits and reverse engineering in general
Packers and Unpackers - Couple of useful packers and unpackers

Virtual Machines

VMWare - The industry standard
Parallels - Apple Mac based virtualisation
Virtual PC - Windows virtualisation
Bochs - Opensource Virtualisation
VirtualBox - Closed and GPL Virtualisation technology

Disk Cloning

ddp - dd-delta-patch for creating diffs to dd images
Norton Ghost - Great disk imaging tool

System Snapshot

Deep Freeze - Freeze the systems configuration to a known good state
Steady State - Snapshot a Windows XP system
Returnil - Return the system to a known good state after reboot
CoreRestore - Hardware device that intercepts disk activity, providing a snapshot ability