IDA Pro is a Windows or Linux hosted multi-processor disassembler and debugger that offers so many features it is hard to describe them all.
http://www.hex-rays.com/idapro/idadown.htm
Do you need to analyze multiple variations of essentially the same program?
Do you need to understand the changes between two versions of a program?
Are you trying to detect code theft?
zynamics BinDiff uses a unique graph-theoretical aproach to allow comparison of executables by identifying identical und similar functions.
http://www.zynamics.com/bindiff.html
Immunity Debugger is a powerful new way to write exploits, analyze malware, and reverse engineer binary files. http://www.immunityinc.com/products-immdbg.shtml
PEiD detects most common packers, cryptors and compilers for PE files. http://www.peid.info/