The ECFP/FCFP license covers the usage of the ECFP and FCFP fingerprints. It also covers all chemical property calculations needed to calculate the FCFP fingerprint, but in a limited mode only.
The Chemical Hashed Fingerprint is free.
The Molecular Descriptors license covers the usage of the BCUT descriptor and the Pharmacophore Fingerprint.
The MACCS-166 license covers the usage of ChemAxon's implementation of the MACCS-166 fingerprint.