What workflow can I use on to extract cartesian coordinates of many molecules from both .spartan and .out (Gaussian) files?
The only tool that I know for reading Spartan files (besides Spartan) is Jmol. With some programming or scripting, you will probably be able to save conformers to other files in a workflow - I don't think there is a pre-existing script.

There are multiple open source tools that read Gaussian output files. I would suggest either:


Open Babel - GUI, command-line and Python
cclib - using Python


For example to extract a bunch of Gaussian files to XYZ Cartesian:

obabel *.log -oxyz -m

The -m flag indicates "multiple" and the -oxyz indicates that you want XYZ-format files. More is in the manual.