A good project tree browser for Emacs?

I haven't tried this one myself yet, but emacs-nav is a new Emacs project browser from Google that seems to have the features you value.

Projectile + NeoTree are my combination of choice.

Projectile just uses your version control system to track files and has an awesome jump to file in project function.

Also, check the notes for integrating the two together.

Speedbar?

If you just want to manage related files, perhaps you would like eproject.