Back when I actually had time to work on ClearTrace I had visions of selling the software. I don't think that's going to happen anytime soon. I don't have time and there's a bug in SMO that causes problems with traces generated on 64-bit servers.
In the meantime, there is additional functionality in the software that people can take advantage of. Under Tools -> Options you can enter "jayhawk" in the Beta Code field. This will allow you to create multiple trace groups. You can use trace groups for anything you'd like. You could create one per server or one per type of trace you run. It's really however you want to use it.
This also allows you to save the trace information that you are loading into the application. You can continue to load new trace files into a trace group. The key thing to remember is to always use unique filenames. If you reuse a filename it will overwrite the existing trace.
I'm not sure how well the application will perform as the database grows larger and larger. I haven't done much testing in that area.
I'm also going to see if I can't get a command line version working sometime in the next few weeks.