Honestly, depends on which docking you are talking about. The mechanics of the software (i.e. the algorithms, scoring functions) depend on its purpose. If you want to do protein-protein docking, Autodock might not be the best option. For protein-ligand docking, it might. You also have protein-nucleic acid, protein-glycan, multiple proteins, etc.

Autodock is a good option for protein-ligand docking. If you want an overview for protein-protein/DNA/etc docking, have a look at these reviews: 1, 2. Nearly all that software is free for academic use.

Autodock is one of the popular softwares available in open-source for docking. Popular commercial ones includes Tripos SYBYL, Discovery studio and schrodinger.

You can find the list of software in wikipage