One of the big differences is that, as far as we know, the CM Organizer is the only one designed specifically for a Charlotte Mason style education. That means you don’t have to try to force your flexible ways into a mold made primarily for tracking attendance, grades, and such.
Another big difference is that the CM Organizer is an online service instead of software you have to mess with installing. We think there are some big advantages to this approach, which we talked about in a couple old blog posts: 5 Reasons the CM Organizer Is an Online Service and Are my school records safe in the CM Organizer?.
Of course, the important thing is to find something that fits your family and style. That’s why we have the Organizer free trial. I would encourage you to take it for spin and also see if Homeschool Tracker has a demo. You might also want to have a look at our tutorial videos if you haven’t already.
Homeschool Tracker has a set of videos for their plus version you can look at too.
Hopefully, there are others here who have tried both and can give some feedback about their experience. By the way, if something fits your family better than what we offer we’re okay with you discussing it here. Please feel free to talk about all the options and we’ll all learn from your experience together.