Mine has got to be the Wydra Boat mod. But mainly because it's fairly broken as is. I spent so much time tinkering with it to get it working better but now it'll do around 40mph on flat water.
I changed the way the prop works so it doesn't stall every time you switch from D to R, I gave it a Neutral gear, I tweaked the values in the "torque converter" to get it to behave more like a real outboard motor would, and I slapped on a turbo for MOAR POWARRRR.
I also shrunk the size of the outriggers (flexbody and JBeam) since they were creating too much drag and slowing me down.
Future ideas? Add the main engine back in and attach the outboard with the trailer hitch slot allowing amphibious travel.
Anyway what are your favorite mods?