Ever wonder how to create tunnels in SC3000? Well its pretty simple if not expensive. First, raise the terrain at the tunnel entrance to as steep as practical using the terrain editing tool. Next, place one rail or road segment at the base of the hill where the entrance is to go. Then starting three squares back from the side of the hill, drag the road/rail creation tool across the starter tile and one tile up the side of the hill (First attachment), then let go. You will be asked if you want to create a tunnel and how much it will cost (1,000 simoleons per square of tunnel).
If you want to create a tunnel underneath of a body of water, pause your simulation then raise the land level in the body of water high enough to create your tunnel as explained above then once the tunnel has been created, lower the land to recreate your body of water (first attachment).
If you pre plan your city at the start of the game and start with a city that is sufficiently above water line, once specific road/rail corridors become heavily congested, you can create a parallel tunnel by dezoning some land at both ends of where you want the tunnel to go and then lowering the elevation of land at the two openings such that you have a steep hill to use as backdrop for the tunnel. Once the tunnel is in place, you can fix up the ends and tie the tunnel into your road/rail network as is necessary. This can be very useful for reducing congestion along your most congested corridors, however, it is also very expensive and shouldn't be done unless you've got simoleons to burn.