If you've been using your cube as much as you should be, the stickers are peeling. If not, your cube is probably significantly better than mine. The stickers were really awful, and I had to do something about it. If you wanted something easier, you could skip right to step 6 and have a black cube, but you don't want that. You want a Gold Cube.
Step 2: Disassemble the Cube.
Twist any face 45 degrees, and lever something between the centre face and an edge face. Pop the edge face out. Once the first Cubelet is away, the rest will follow it out fairly easily.
Step 3: Wash the Cubelets.
In the sink.
Step 4: Set up a paint station.
A box with a stick through it will serve as a convenient place to hang the Cubelets while they're painted. It should be noted that I abandoned this method about halfway through because I realized that the bottoms of the Cubelets weren't getting enough paint. I resorted to holding them above my head and painting them that way. If you design your paint station with this in mind I'm sure you can work around it, and keep your fingers paint-free.
Step 5: Paint the Cubelets.
Now take sublime pleasure in the moment as you are priviledged to witness your precious Cubelets as they metamorphose from the anthracite coloured lumps that they were, into the shining and glorious beacons of Nerdcore that they are destined to become.
Step 6: Drill dots.
Clamp the Cubelets down. Drill a small depression, one edge at a time. Take care not to drill too deeply, as a hole is far more difficult to fill than a dot.
Step 7: Paint dots.
I used basic student-grade acryllic paints. I'm sure anything you have (that isn't water soluble) will do fine.
Step 8: Reassemble the cube.
This is the reverse process from disassembling the cube. Start by turning one of the core faces 45 degrees and slip in an edge piece. Just keep on adding Cubelets, and building faces until there's only one Cubelet left. It won't go in unless the final face is twisted 45 degrees.