To paint fondant gold for ribbons, I used Gold Pearl dust mixed with Vanilla (or vodka). I imagine you can buy any colour dust and use it to paint. If painting large areas, there are sprays you can use. I know Duff's graffiti spray is supposed to be good (I"ve never used the sprays before!)
When coloring flowers, I use the dusts then steam them to set the dust. The dusts are very true to color and I love them. As for just painting on fondant I like the dusts mixed with vodka. It works well but I know some use the Ameri-color gels too and they work well too. As long as you use an alcohol base and not a water base you should be fine with almost any color... not the little squirt bottles from the grocery store though!