Disassemblers: IDAPro (Tutorials ) , Win32dasm , YASM
File Analysis: PEiD , HexWorkshop , HIEW , PeDump and PE Overview
Packers/Encoders: UPX , UUDeview , Universal Extractor , ASPack , Unpacking Gods , ExeTools
Malware Analysis - iDefense toolset
General Sites: RCE Forums R-E.net
Black-Box Methodology