For a clear color, more like a watercolor, you can use:
-Straight liquid food coloring
-Corn syrup with food coloring
-Vodka with food coloring or petal dusts
-Piping gel with food coloring
For slightly more opaque colors you can mix white food color (titanium dioxide) with food coloring or petal dusts.
But for colors that need to be fairly opaque, you have to use a base that's opaque to begin with. This limits you to things that won't dissolve the color so much as just provide a medium to float it on the surface of whatever you're painting.
That basically means that you need something oil-based, which ends up being crisco or another type of shortening, and buttercream.
You can dissolve fondant until it gets to a paintable consistency then mix a color into it, but that's a sticky mess, and as the liquid in it evaporates you'll have to add more to keep the consistency.
The easiest thing to do is to start with some shortening and add petal dust or oil-based candy colors to it. You can use this like an oil paint, and it remains pretty opaque because it sits on the surface of the thing that you applied it to unless you rub it off. The container of yellow above is crisco with yellow petal dust mixed into it. You can also use buttercream to do this if you're painting directly onto a buttercream cake, then thin it out with corn syrup to get the consistency you need. I did this one years ago with the buttercream as a base, since it was a buttercream cake.
When I put it on this gumpaste bamboo it covered the darker green color nicely, which a more transparent color wouldn't do.
After painting it on you can smooth it out with the brush or a fingertip to adjust the thickness of it.
I also put a little bit of the yellow in the center of the purple wafer paper orchids I'd made for the cake, just to break up the purple a little. Since the "paint" is oil-based it won't dissolve the paper, so you can also use it to color wafer paper by smearing it on the sheet. It's good for stencilling, too, since it's a pretty firm consistency and wont' move once you put it on. I'd only use that on fondant, though, if you're going to stencil on buttercream use buttercream to do that. Tastes better.
Kara Buntin owns A Cake To Remember LLC, custom wedding cakes in Richmond VA