What you might want to do is have the option for a config file, if found, to be read that can have some other options.
So, if your first disk is Pirates_disk1.adf, you could create a file called Pirates_disk1.cfg that would have game specific configs. (Which kickstart, PAL/NTSC, memory, etc..)
Then, your script could just do something like:
if [ -f "$filename".cfg ]
..and you can load the options if they exist.
That way, most of your games would work with the defaults (KS 1.3, 512K chip, 512K fast), but you can add configs for the games that need it.
An nicer way might be a database with pre-configured options, based on tosec names probably.
And a web service for said configs would be REALLY nice, but I'm thinking that's WAY too complicated... :-)
desiv