Jay Collett used the .NET library created by Jean-Francois Talbot (also in the ThingM github) to build a nice & small system tray app that does exactly what he wants.
Read about it here:
Jay includes all the source code so you can see how it's done and modify it to your own tastes.
One of the downsides you might say of the Blink1Control app is it attempts to address the needs of many different use cases. If you want something very specific, building your own custom thing is the way to go. This is why we like Open Source so much: it let's people customize their products to fit their lives.