I'm not sure what you mean by non-popular. Much that is popular on HN is unknown to most people. My take:

* Multiping: Simple utility that pings multiple hosts, and displays the results on a zoomable side-scrolling graphs that sync by time. Thus you can immediatley see, for example: At 08:06:33, of the hosts on my route to the Internet, the local firewall responds, as does my ISP's gateway, but the next hop and everything past it are timing out; and the same thing happened 4 times in the last week for periods of 2, 18, 6, and 11 minutes, always around 8am.

Just look at a screenshot (I'm talking about the three horizontal graphs in the middle, you can have a many as you want of those):

http://www.multiping.com/images/multiping_screenshot_big1.pn...

* OpenBSD: I just installed it for the first time. Despite it's reputation as an ubergeek tool, it's shockingly, exceptionally, elegantly easy to install (for technical folks who know what DHCP and MBR are). The documentation is amazing, so far, and if the rest of the experience is like the install, I'll be very happy. A pleasure to drive.

Some (maybe) lesser known gems for Windows machines:

http://www.peazip.org/ - Zipping/Unzipping utility, better than WinRAR or 7-Zip

http://implbits.com/products/hashtab/ - Shell extension that adds a panel in the file properties window that can compute and compare a hash against many different hash functions

http://mactype.net/ - Shell extension that gives various options to modify Windows' anti-aliasing scheme. Useful if you're not a fan of TrueType's look. Can cause noticeable lag and drawing issues on some less powerful systems, though

http://cmder.net/ - Alternative, more-featured terminal emulator for windows (works with both Cmd/PowerShell)