Mythmoor has the Kingdom Sails server-side mod that lets you change ship sails. Simply craft a new sail with a needle and square pieces of cloth. To remove a kingdom sail, right click and use the menu option. Sails can also be dyed.

The kingdoms are as follows. Ignore the brown area on the lower right of the texture.

Kingdom	Sail
Abralon
Apocalypse Order
Black Legion
Dragon Kingdom
Dreadnought
Ebonaura
Empire of Mol-Rehan
Freedom
Horde of the Summoned
Jenn-Kellon
Kingdom of Sol
Legion of Anubis
Macedonia
Mol-Rehan
Pandemonium
Commonwealth
Crusaders
The Rome Republic
Valhalla Descendants
Valhalla
Wurm University