I used red with a metallic silver outline to match my black & red tank with silver coach lines. Gold is very popular. Be sure to buy the ultra-fine tip for precision, and take your time because goofs are a bitch to correct. My wife and daughter did mine because they have steadier hands. The earlier seats (mine is an '06) had the border around the logo embossed so it was really easy to chase the outline. Later seats have the logo embossed flat without the border, and of course the logo itself is slightly different. Mine took two coats to give it a nice look, and I've touched it up once since it was first done.
I think painting the seat logo is one of the easiest and cheapest mods with a big visual impact and splash of individual style.