Perftree is a debugger that compares your perft calculations to the ones generated by Stockfish... and that's basically all that it does. Give it an initial state and a perft depth, and it will help you walk the tree and compare the results at each node, highlighting the differences so you can quickly figure out where your missed and illegal moves are.
Despite being so simple, I have found it incredibly useful in practice. It does most of the work that you'd have to do manually, while staying out of the way and letting you explore the tree at your own pace. If you're interested in trying it, you can find some more documentation and the source code on GitHub. I'm working on getting some binaries released as well, for those of you who prefer that.
Here is a demo of me using it against my engine, which still has some pretty significant bugs: