Compared to WEKA (http://www.cs.waikato.ac.nz/ml/weka/), waffles look inferior. Weka has a much wider variety of classifiers and filters to play with.
One of the cool things they've taken the trouble to do is to make sure that almost all functionality is accessible from the command line.
As such WEKA is easily scriptable. This is great for integration into bigger projects. It can easily be chained like standard unix tools; I've used this functionality in projects with good success.
I'll have a look at the underlying C++ classes API (http://waffles.sourceforge.net/apidoc/html/index.html).