Best way - Fill it with a solid piece of wood, glued in with wood glue, sand it level, fill any cracks with wood filler (minimal hopefully), sand it again and refinish the guitar.
Easiest way - Get some pickguard material, cut it slightly larger than the hole and screw it on. You could always airbrush a design on the cover too....or maybe a cool sticker would work if desired. If you're feeling really artistic, you could even cut the material in a shape, like a bat or something. But of course, just plain would suit the purpose - and be the easiest.
Cheapest way (my pick) - leave the neck pickup in it - or take out the EMG and throw in a cheapo humbucker. Any alterations will probably hurt the value of your guitar(s) if you ever decide to part with them. But that's up to you.