Klipper - Clipboard manager for Linux. It's part of KDE so I'm not sure if it counts but it doesn't seem to be well known. Basically the same as Ditto for Linux but a bit clunkier.
7+ Taskbar Tweaker - Tool that modifies the Windows taskbar. My favorite two features: 1. Hiding the Windows logo/start button so Win+1 correlates with the first icon, Win+2 with the second, etc. 2. Making it such that if I click an application icon with multiple windows, the first window will just come to the front (and the second if the first is already at the front, etc.) instead of having to click from a list of windows.
SharpKeys - Windows tool to remap keyboard keys. Equivalent to using the Registry but more pleasant.