Looking at your map, it looks like you've already got a pretty good elevation setup. For an easy coloring technique that shouldn't mute your details would be to try some layers in gimp with different blending modes:
- Open Gimp
- Start with your uncolored map as the bottom layer.
- Add a new layer - bucket fill (Shift-B) it with the color you want to add.
- Change the layer's blend mode to Overlay or Soft Light
- Add a Layer Mask - start with full opacity (if you want to keep most of the color) or full transparency (if you only want a little color)
- Use a grungy-looking brush (I'm fond of Big Galaxy) to paint black or white on the layer mask - white where you want your color, black where you don't want it
You can also fiddle with the brush opacity - I like to start light (maybe 30%) and apply some jitter - keeps my OCD tendencies from making too many obviously regular formations. To add more colors, just add more layers for each color, and repeat the painting process. This method also makes it MUCH easier to correct mistakes and make small tweaks without resorting to endless undo-redo cycles.
Another option, since this is "Mars with Water" (and presumable has a hydrological cycle i.e. rain) - depending on your elevation layout's format, you could try importing it into Wilbur and running some Precipitation or Erosion cycles to add some rivers and other effects.
There's a huge variation in map styles and techniques out there - maybe if you could post some links to what style you're looking for, someone here could point you at a technique or tutorial that could achieve those effects. Recently, I've been a huge fan of arsheesh's Eriond tutorial.
I may also take a stab and see what I can do along these lines... always liked the idea of playing around on Mars.
EDIT: Found a Mars height map online, did a little playing around, and came up with this result:
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