Each higher class can have any upgrade any lower can have.

Class 1:

Class 1 ships are not capable of sea travel (ocean squares), but they can
access the swamps in turn. These ships are not really good for more than
learning basic sailing. A class 1 ship comes with space for max. 5 sailors
(practically one free sailor quarters), helm for commanding the ship and a
gangway for entrance and exit.

Class 1 modules:

Console:

A class 1 ship can support a console, with which you can view some crucial
info (status, condition,  attached modules). Every ship used for sailing
should have one. Silver lake has some extra functions available for you to buy
to your ship's console to toggle speed of sailing and height of flying.

Class 2:

Class 2 ships are the basic affordable ship type, and you can sail also ocean
squares with them. They  are also the smallest craft capable of going to the
few areas where a ship is required to enter. However,  you can no longer sail
the swamps with these ships.

Class 2 modules:

Captain's cabin:

Captain's cabin enables the autopilot functions of a ship, once you hire a
navigator (cost 100 gp - 2.5m depending on his level). With navigator you can
memorize locations much like location memory and then sail to these locations
later on. A class 2 ship has space for 1 bookcase with ~30 possible locations.
Higher level navigators enable better pathfinding and better chance for
succesfully memorizing locations.

Cargo hold:

Usually you cannot drop anything while aboard a ship (or it will washed
outside the ship). However, a cargo hold can carry up to ~800 kg of stuff, but
YOU CANNOT SAVE ANYTHING OVER BOOTS THERE. A cargo hold provides also
additional way outside the ship, and you can also install one workbench /
cargo hold. A class 2 ship supports only one cargo hold.

Crow's nest:

From the crow's nest you can view a bit larger map compared to the deck.

Galley:

Galley can support a food locker and a drinks cabinet which you can buy from
silver lake. It can increase your crew's morale on long trips to have some
food with. However, the morale code is not mostly implemented yet.

Sailors' quarters:

A sailors quarters can provide room for extra 5 sailors to hasten the movement
of a ship. A class 2 ship can have a total of 2 of sailors' quarters, and no
other crew quarters are available.

Class 3

Class 3 ships are the smallest of the luxury ships. They are the fastest ships
available, but lack some of the abilities and firepower the higher classes can
have. The major class 3 boon is the ability to add mages and fly. A class 3
ship can support up to 8 sets of crew quarters, of which max. 3 can be
sailors' quarters, 3 speed magi quarters, 2 lift magi quarters and 1 defense
magi quarters. A class 3 ship's captain's cabin can contain up to 2 bookcases
(you can buy these at silver lake) and 2 cargo holds.

Lounge:

Lounge is a room where you can buy some regeneration promoting things like a
crystal and a fireplace. Every self- respecting captain should of course have
a place for his guests too :)

Lift magi quarters:

Lift magi quarters can house up to 5 lift magi. The more you get of these, the
higher the ground the ship can fly over.

Speed magi quarters:

Speed magi quarters can house up to 5 speed magi. Speed magi hasten your ship
while flying (without these, the flying is painfully slow).

Defense magi quarters:

Defense magi quarters can house up to 5 defense magi. Defense magi create a
defensive shield around your ship, protecting it from damage (as of writing of
this, combat is still unimplemented).

Class 4

Class 4 ships are the 'merchantmen' which have excellent storage capacity, and
can be used as mobile refineries. Class 4 ships are bit slower than class 3,
but they can have more crew and thus fly higher than class 3. They also
support the portal room.

Class 4 ships can have up to 14 crew quarters, of which 4 sailors, 4 speed, 4
lift, 2 defense and 2 assault. Captain's cabin can have up to 4 bookcases.
These ships have a maximum of 5 cargo holds. 

Teleportation chamber:

As ships are otherwise no-summon zone, teleportation chamber allows people to
go to the ship (other people too) with teleportation spells. You can also buy
a church portal to the chamber. 

Assault magi quarters:

These quarters can house up to 5 assault magi. They are of no use as of
writing of this because there is no combat.