Captain's cabin

The most luxurious place in a ship is the captain's quarters. In smaller ships the captain usually don't have the luxury to have private quarters, instead the officers share the quarters with him.

Bookcase

Bookcases are very useful for storing maps which your navigator can use for piloting the ship. You must already have a Captain's Cabin, and there is a limit on how many bookcases a particular class of ship may have.

Bookcases store the maps that are used for the autocruise feature created by ship survey. They used to be limited to 32 maps apiece, but this number was raised with the expansion of the realms to 60. To get new blank maps, you need to insert <spell scroll> into the bookcase. From Carl at Captain's Rest, silverlake for ~66k gold each. You can also have one removed for ~2k gold.

Dimensional vault

Bob Stance will install one of these special vaults in any ship that is at least Class 3 and has a Captain's cabin. They function as normal chests, except they can't be moved and by default only the captain can ever open them. At a cost of (100k * number of current slots + 100k), this is a secure but very expensive way to permanently store items onboard a vessel.

Elixir cabinet

These cabinets store special elixirs which help heal or boost your crew. These elixers are going to be fairly important for anyone who gets involved in combat but quite expensive (~80k/elixir). Each cabinet has space for ten elixers, and up to four of these cabinets can be stacked in a captains cabin.