This answer.

Use the scoring function of Autodock. If you can (not sure if Autodock allows that) cluster your solutions and look at the average score of the clusters (or at the average of the top 5 or 10 solutions in each cluster), as this might filter some awkward high scoring isolated solutions.

If you have two clusters or solutions that are close in score, have a look at the structures yourself. Do they make sense? Do they match what they should from the biological role of the protein-ligand complex?

Energy is important, and if you see good interactions (Hbonds, no steric clashes) you can hypothesize than your docking pose is correct.

However, i am not an expert in the field. I just know the basics and you could have learn all that i said by reading the faq of Autodock http://autodock.scripps.edu/faqs-help/faq/what-should-i-look-for-when-i-visualize-a-docked-compound

Generally, pose with the lowest docking energy (binding free energy) consider as the best conformation, but you should also check other criteria ; RMSD and the number of interacting residues/ hydrogen bonding, which are very important. The best conformation should follow all these three criteria. And also verify your best pose with other molecular docking tools, Dock6, swissdock, Hex, dock, or Audotock Vina (new version of Audock) etc.