Something I nicked from Mick Bryan - one of those blindingly obvious ideas that you kick yourself for not thinking of before.
Cut a small piece of brown paper (dimensions not micrometer critical) large enough to cover those annoying holes in the baseboard you get when mounting Peco point motors directly to the underside of Peco points. Make a little slit in the middle for the operating rod.
Sandwich it between the motor and the point when joining them together. The operating rod needs to pass cleanly through the slit you cut, but the fixing lugs for the motor can be just pushed through the brown paper. Finesse is not required.
The brown paper hides the hole quite well against cork and will be invisible once ballasted. When everything is to my satisfaction I wipe a dab of white glue under the edge of the paper to hold it down.
A variation on the theme can be used to fit paper to existing installations. Slightly more complex shapes need to be cut and then slid under the point, loosening any track pins as required.
On a related note, you can't pour ballast onto the average layout for too long before you realise you're getting a shoe full of the stuff - closer inspection reveals it's running down the wiring holes like sand through an hour-glass. The solution, obviously, is to stop up the holes somehow, and there's a variety of ways to do this. My preferred option is to break off little beads of expanded polystyrene from spare pieces of packing material and wedge them down the holes with the tip of a screwdriver. As long as you take care not to attack the wire with the screwdriver this is a quick and simple solution - the polystyrene will easily mould itself to fill the hole around the wire.