UnxUtils: This is a port of various gnu shell utilities based on msvcrt.dll so it understands native windows paths - i.e. you don't need to map to a
/cygdrive path. This is a key advantage over Cygwin if you have to interact with native windows commands or homebrew CL utilities.
Strings: is a very good way to scrounge through files for items of text. Many, many uses.
Flex: Really designed for writing lexical analysers, with a little bodge artistry and a C compiler it can be used as an uber-grep. I don't use it all that often but it can come in surprisingly handy in that role.
Fetchmail and Procmail: Core of my email system for well over a decade, since I had dial-up internet connectivity. If it ain't broke ...
rdesktop: an open source RDP (terminal services) client that works surprisingly well.
PythonWin:, particularly as packaged in Activestate Python. Python on Windows works a lot better than you might think. When used with COM Makepy it's really good for scripting COM APIs.
Wget: an exceedingly useful FTP/HTTP downloading tool.
Leafnode: if you still read any of the newsgroups that still have decent active traffic this is quite a good way to do it. Again, a bit of legacy from my dialup days but it still gets used on occasion.
Abiword and Gnumeric: full featured wordprocessing and spreadsheet software that's far leaner and meaner than OpenOffice.
Xfig: Visio type diagramming tool with an odd user interface. Once you get used to the paradigm it's much easier on my poor old mouse hand than a modern direct maniulation interface. Worth a mention for the ergonomics.
Tcl/Tk: Overshadowed by Perl and Python, Tcl is very easy to embed C code into - it was designed specifically for embedding. Surprisingly useful nonetheless, and the Tk toolkit is very easy to whip up a GUI with. Modern versions support theming so your applications no longer have to look like Motif.
Ghostscript: One of the great unsung heroes of the open-source world. A free postscript interpreter with a whole ecosystem of derived items - PS and PDF viewers, PDF creation tools, printer RIPs and all sorts of Postscript conversion tools. Perhaps most widely used outside open-source circles (if not actively credited) in its role in the back-end of PDFCreator
That's just a sampling of the obscure stuff without mentioning Vim, LaTeX, Firefox, python, gcc, gtk & qt and the Berkeley TCP stack - to name but a few.