Since you're currently the keeper of many of XPort's projects I thought you'd be the person to make this request to. Would it be possible for future releases of these emulators to remember the last used game config settings as the defaults? The current builds only remember them until the next time the emulator is started.
The main reason for this is that I feel some of the current defaults aren't at all optimal. For example, in MednafenX-NES the NTSC Scanline settings are configured by default to cut 8 pixels from both the top and bottom of the screen. This means you lose half the floor on SMB unless you change these settings. Also in XboyAdvance the optimal frameskip setting is always 9 (the maximum) since the emulator only skips as many frames as it needs to.
I could go on about various things I have to set every time a play a new game so it would be great to either have the settings remembered between sessions or least come up with a more optimal set of defaults.