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That would help so much when dealing with complicated circuits.

Thank you for your suggestion.
In complicated circuits you actually probably using multibit wires so it is not that obvious how to color them. On the other hand you can always click the wire and see what signal it is carrying on. If you need to see some specific set of wires in action you can always connect probes or LEDs on them. The reason I hesitant on coloring wires is performance. It will significantly slow it down if all wires are showing states.
Hope this making sense to you.

Well, at least light upp the complete wire when you click on it, Makes it easier to see if everything is wired correctly

Well atleast light upp the complet connection, all wires included in a connection when som part of it is clicked, now the only thing that is colored is the segment.

It is actually already implemented. To select the all connected wires, click them while holding Shift key.
There are many menu items under Edit menu that help to see what is connected or what not.
You can read help pages for more details. Especially:
http://logiccircuit.org/edit.html
and
http://logiccircuit.org/advanced.html