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CLCL is better than ClipX, IMO.
IzArc is better than WinRAR or 7-zip, IMO (someone else also suggested this)
Cygwin makes available some of these tools, such as locate(1), OpenSSH, GPG, Vim, isotools, diff(1), and xmllint. Others mentioned this, but the point needs to be reiterated.
PDFtk and Multivalent are fairly invaluable to me when working with PDFs
I concur that Avira AntiVir and HijackThis are the best entry-level tools, however they can't and shouldn't be completely relied upon. McAfee Stinger is often still sometimes useful as another entry-level tool. WinHex and IceSword are examples of mid-level tools, but the best tools are commercial and very advanced (e.g. HBGary, MANDIANT, etc)
IDA Pro (as someone mentioned) is basically the de-facto disassembler, but it's not so great as a debugger. Various debuggers exist, but Syser, OllyDbg, Immunity Debugger, and WinDbg are some of the better ones. .NET Reflector with Deblector is a great debugger for CLR executables
I often bounce between Firefox, IE, and Chrome. Firefox has many benefits, but is much more useful with FireBug/Firecookie/YSlow, All-in-One Gestures, Greasemonkey, and SwitchProxy (for Burp Suite)
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