I do this all the time with mameWAH. Many of my emulators don't easily allow or even allow at all for saving the screenshot in PNG format in a specified directory. As a result, I call these emulators with a batch file that is responsible for finding the image, wherever the emulator drops it, converts it to PNG if necessary, fixes the filename if necessary, and moves it to the SNAP folder. With mamewah, I've only had trouble in the event that I am not using a specified extension (ala *), and have to work a little magic in the batch file to figure out the extension. Other than that, it's trivial and works great.
Chemame