Hi,
For all who want a real depressing dark Fleet in night-black, or a real gay Advent cruiser in pink here is just a simple instruction for changing the selectable player-colors.
The file is located in "..\Sins of a Solar Empire\Window\Colors.color"
open it with a text editor of your choice and you'll see:
-------------------------------------------------
TXT
positive ff89D217
negative ffff2a00
notAvailable ffCCCCCC
highlight ffFFC705
warning ffFF891D
unknown ffa8a8a8
normal ffffffff
normalInverted ff000000
subValue ff7E7E7E
playerColor:0 ffF8F8FF
playerColor:1 ff0000FF
playerColor:2 ffFFD700
playerColor:3 ff8FD81D
playerColor:4 ff007037
playerColor:5 ff0EADFF
playerColor:6 ff0044AE
playerColor:7 ffFF87FF
playerColor:8 ff8822B7
playerColor:9 ff00FFFF
playerColor:NPC ffbdbdbd
chatMessage:ALL ffffffff
.
.
.
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as you might guess you have to change the last 6 digits of "playerColor:X"
"playerColor:0 ff000000" would render the first selectable color black (quite difficult to see on the star chart though...)

Here you can find nearly every thinkable color as hex code:
http://www.december.com/html/spec/colorhex.html