I did a quick search but i had some interesting ideas.
1) being able to color coordinate the link tool for organization sake. So basically be able to color all active links by changing the color via the scroll wheel and alt+MMB
2) I don't know about you but i get lost while diggin tunnels like a mole rat. So maybe a quick tag system. like just a simple spray paint can with a few simple makers like
red "X" (dead end)
Blue arrow (hitting R will rotate the direction by 90 degrees. so you can place on wall or floor. )
green Circle (ore here)
white square (ore somewhere around here)
Paint is only seen by org and player.
cant paint on ships only earth, trees, rocks. simple things like that.