that is a hard question, I'll have to find some time to make a comparison, but here are few points:
Paint.COM:
* is not .net based and hence more portable, faster and less resource intensive,
* already has features that are planned fro Paint.net 4.0 like layer effects (
video) or soft selections,
* has more advanced drawing tools - you can adjust last drawn shape, use non-integral coordinates, define custom fill gradients or sRGB optimized blending
* good Photoshop .8bf plug-in compatibility
Paint.NET:
* older and more established -> more tutorials and people, who can give you an advice
* more effects and native plug-ins created by community
* simpler user interface
There is much more differences, but for starters it should be enough...

please note that I am the author and my opinion is biased