Is there a way to save preferences for import/exporters? I often use the .fbx export plugin in Blender, and every time I must disable the apply scale and enable selected only options. I realise that not everyone wants these settings enabled by default, but is there a way to save the settings so that I never have to do it again?

Note: I can probably edit the script to change the default, but I have a strong feeling that it can be done and saved with my user prefs somehow.
Yes, you can use operator presets. (Press the + icon to the right hand side of Operator Presets dropdown).