Any free tool for Calculating Gasteiger-Hückel charges for ligands?
The method is not fully published according to Gasteiger.

There is an online server for PETRA run by the Gasteiger group, and in principal, it's available from Molecular Networks. I note that PETRA is no longer listed on the products page, but it's probably part of some other product now.

The open source CDK package has an implementation of the PEPE method, although I don't know if it has been validated against Gasteiger's code.