I use Query Tracker. (I have a subscription, but there is a free version.)
I have not heard of Duotrope, but I gather that many writers use it and are happy with it. Starting in January, you will need a subscription. I suspect that many sites that have been free will be adopting this model soon.
The blog post below is the first in a series evaluating whether or not the $50 annual toll will be worth the return. In this first installment, Nathaniel Tower includes a useful Excel template for tracking submissions.