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:

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