If you want to expand on this idea a bit, here are some more ambitious ideas:
By default, Daphne could parse ini files for each individual game first, then check dapinput.ini. For example, for Dragon's Lair, lair.ini would be searched for first. If it wasn't found, then dapinput.ini would be used. Specifying a file on the command line (-input reverseY.ini) would override these settings.
This is actually why I didn't volunteer to do it myself. Handling the first part (being able to specify a different input file on the command line) was a no-brainer, but the rest would take more time than I have right now (work is calling).
I have to confess this grows out of a desire to (someday) have daphne parse an ini file for each game for other settings as well. And I further have to confess that grows out of a desire to have daphne behave more like MAME (although I have no desire to see Daphne merged with Daphne -- I like the Daphne team way too much for that to happen). Users of DaphneLoader don't need this functionality (since DaphneLoader stores settings for individual games), but I use a common frontend for all of my emulators, so I can't use DaphneLoader (although I still use it for testing purposes and as a quick and dirty way to get dip switch settings).
-etumor
Supercade: Classic Arcade System