Don't know about a comprehensive list but perhaps this resource is useful?

There are thousands, if not tens of thousands, which have been published. Look into any JCICS issue from the 80's and you will find again a paper, or two, or more, by the "usual suspects" inventing another 50 new graph-based descriptors by squaring one of the parameters used in the previous publication (and listing some values for saturated hydrocarbons as the only covered structure class).

My advice: Use any of the standard packages (Dragon, Mold2, etc., or the appropriate component from any larger modeling package) and you are set. You won't get better results by adding another 1000 highly correlated descriptors.

I definitely recommend book Molecular Descriptors for Chemoinformatics by Roberto Todeschini. It became handbook for molecular descriptors - you will find description, reference and mathematical explanation of descriptor.

I would suggest looking at ChEBI, but you may also want to look at the list of databases maintained/assembled by the cheminformatics team at EBI. They also have some neat exploratory tools, like plugins for Cytoscape, and many other tools so you might want to search through the related pages at EBI.