I tend to favor phosphoric acid. I posted some photos of a good example of results from phosphoric acid here: Questions for Evaporust Users
I've never used muriatic acid, but I'm sure it works well too.
As an alternative, citric acid works in a pinch as well. Here's an example from when I used citric acid to treat some rust in the inner structure of my dedklid: Inner Panel Rust Treatment - Decklid
