Surprised to see no mention of the 'top' deck to 'bottom' deck gun jump for the Junker in here--maybe it's too simple? Though I do rarely see it done.
Both the railing and marks on the hull-deck on either the right or left side of the junker provide an easy frame of reference for the position of the lower deck guns. By jumping over the railing where the second to last 'spike' sticks up (you know, the |--|--|--| on either side?) and holding back towards the ship, you can easily land on the gun or gundeck below, allowing you to slip onto the main engine or lower deck guns very quickly from the upper deck. Once you're used to this, it's not hard to make the jump from different angles, as well.
Also, someone mentioned the rigging on the Galleon above--you can actually climb around in a lot of the rigging in a bunch of the ships. With many it's of limited use, although I suppose there could be applications for pre-battle spotting positions (I know I love to climb in the rigging of the Junker for this myself.) Almost tempted to start a thread about it, but I dunno if it'd be much use to anyone lol.