Killing Enemy Transports
Just right click on the enemy transport and...almost forget about it. You will sink the transport 95% plus, of the time. The only way to stop your destroyer is to kill it, or to hide where the destroyer can't go. So just watch it out of the corner of your eye to make sure it does it's job. Some very good players will repair their transport to give themselves enough time to come sink the destroyer, so be careful. The 3 pictures below demonstrate a hunted enemy transport that has been locked onto.
You can see how my zeppelin spotted the transport in picture 1. Even though my destroyer is half way across the map, I still right click to attack on it, as it leaves the view of my zep. The chase is then on as the transport is locked onto, and is almost as good as dead...
Of course, the best thing to do is to use a zeppelin over the enemy shipyard, so you can sink any transports as soon as they pop out. Unfortunately, the game isn't always so easy, and sometimes you have to hit a moving target.
The trick to sinking a moving transport is to let it get by you first. If you've read the Jugg Battles page, you know how juggs always over shoot an oncoming target, but hit a target that is moving away from them. Well the same thing applies here. Let the transport move by you, and click to attack as soon as it does. If you timed it right, your jugg(s) should hit the transport pretty hard, hopefully sinking it.
This is not easy to do, especially on the fastest speed setting. If you have to do this on that speed, click on the transport right as it gets to you. This should give your juggs enough time to finish their movement and get a shot off before the transport flies right by you. You have much more room for error when doing this in a ladder game.
Again, right clicking on an enemy transport will do the trick. Subs are fast, and can follow the transport all over the map. Just lock on and let them go to work. Of course, the best way to use them is to sit by the enemy yards out of range of anything they might attack. Then you can let the enemy load up the sub, and as the last units are getting on, you go attack. Most of the time, players will panic, and try to move the transport away, which is just what you want...
As soon as the enemy transport was built in the above example, I went in for the kill. Immediately after, I will move my subs back again so the enemy doesn't know where they are. Staying out of range and killing transports as they load up works extremely well when neither of you went ships at the start (this happens a lot on High Seas Combat). You can also leave a couple of subs out where you think the transport will pass by. This way, if the enemy is very fast and gets the transport away with a few hit points left, your waiting subs will finish it off.
If the enemy is killing any subs that come around his shipyard area, then you can also make a row of subs just out of range of any blizzard or decay from the enemy. A transport that runs into a line of subs will have to travel to the end of the line to get around (it will not go overtop of the subs). This is sure-death for them, as all of your subs will get to fire at the enemy.
This time, the enemy caught me in a narrow part of this map, and blocks me off from the left side. If you have units on your transport, you could use the unload button to do the transport slide right over top, but you usually run into a blockadeunexpectedlyy.