Well, I think I'm making progress in the water department.
I started by "flattening" out my water tile. The IM script Redrobes provided didn't work out very well for me (might just be my result with this tile).
Before:
After:
Yikes! Even more contrast in that one. I eventually just resorted to tweaking the color levels by hand with The Gimp, and got this (this is actually my second version. The first was a bit more turquoise until I turned the blue back up. See below):
When combined with a semi-transparent cloud render as Midgardsormr suggests, here's what I got:
I didn't like the turq color, nor did I feel there was enough "noise" from that cloud, so I tweaked a bit more and came up with this:
You can still see the water "pattern" if you look for it, though.