We don't have any docs that explain what options you can use in the conf.json file. We do provide an example file, but that's pretty much it.
It'd be a good start to document the config options that are currently built into JSDoc and its accompanying plugins. These aren't centralized at all, so you'll have to sift through the code to find them.
Eventually we should create a centralized JSDoc module that knows about all of the built-in config options. We should also give plugin authors a way to indicate which config options a plugin uses. That'll require a variety of code changes, so it won't happen anytime soon.