My favorite keyboard mod? By far it has to be the wood cases I've made for my Pure. I love my spring swaps, my lubing, my fixed up RK-9000, by colorful QFR, and so on, but nothing has so fundamentally changed my enjoyment of a keyboard like building a wooden case for one. There's just something about the sound and feel of a keyboard in a wooden case that is so much nicer to me. The suede lining doesn't hurt either.
Edit: I'd also like to add keycap crafting, be it resin, wood, or metal, as my most fun mods and a stem mod on a caps lock as my biggest PITA mod. I'd rather lube enough switches for another two 60% keyboards than do another stem mod.