I know I've only posted mostly questions, and have a WIP in progress to be posted (To moderators, I realized too late about the approval needed! I didn't realize I posted it 3 times, I wasn't looking when the re-direct was coming up because I was bouncing between screens! My most sincere appologies!) But while dinking about, I made some discoveries and as I was not able to find what I needed on the forum for this, experimentation seems to have won out. So I present, Water levels by Levels. Because Redundant title is redundant.

As you see below, we have a cut away of my coast on the southwest. The coast is lighter with a fairly dark portion going into the Bay of Obvious Gamer's World Map. The color was not done with the textures, nor was it done with the burn tools (this was done with Photoshop, so you know but programs like GIMP that can utilize layers and mask layers should be able to replicate as well.)

Click image for larger version. 

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ID:	51108 Before levels shading. Click image for larger version. 

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ID:	51107 After levels shading.

Step 1: Place a basic background with a color for the ocean that you want to work with, this can easily be done by a simple fill layer with the paint bucket tool, to make sure things stay a general uniform color, throughout, while you darken spots you can make a color overlay effect on the layer.
Step 2: In photoshop go to the Create a new fill or adjustment layer button.
Step 3: Select Levels
Step 4: In the levels window that will appear, drag the black arrow on the left towards the right until the levels are darkened to a point you feel good for dark water.
Step 5: Select the blend mode for the layer and change from normal to Color Burn
Step 6: On the layer panel, select the mask for the layer, and enter in CTRL+I - This will effectively reverse the mask to make the burn mask invisible.
Step 7: Now for painting, a good one, in my opinion, is a standard brush 'Watercolor Heavy Loaded' it works just like a watercolor painting brush that is drippingly loaded.
Step 7.5: Make sure your Strength is set to 20-30%, this keeps from immediately filling an area with 'paint'
Step 8: Depending on the size of the area you're working with, you can zoom out and blow up the brush large to rough out the start of the deep water, leaving lighter water near the coasts and slightly darker heading into some of the bays or areas where there might be ships traveling. If you have a pressure sensing wacom 20+ is optimal as it works like an airbrush at times. For mouse painting the brush strength may be better at 20% or a little lower to give you room to wiggle some of the tough spots.
Step 9: Continue to paint over darker portions you want to be deeper, if the deep water is not dark enough - and painting does not darken it further, you can always adjust the levels mask layer as needed, but be careful because like hair grease - a little dab will do you, at least most of the time.

But that is, essentially, that. For some it might be too slow, but I like 'clay working' with my mapping as I (and likely many others before me probably) call it. I like to use levels layers utilizing a bevel method most effectively tutorialized by others before me and then using the push tool to fingerpaint it around for an organic texture. This combined with subtle shifts in water color/depth done through the levels can make those looking for something more realistic to have a nice pop to it.