I loved an estimation tool called Construx Estimate, by Steve McConnell. The few times I used it it was far more accurate than the other estimation techniques we were using at the time.
https://web.archive.org/web/20170920093850/https://www.const...
https://web.archive.org/web/20170920093850/https://www.const...
This is more like an issue tracker/project planner with statistical modeling capabilities built-in, I don't know if it's doing the same thing under the hood, this is part of their "special sauce"