PHost 4 introduces per-ship hull functionalities. Originally, ship abilities were tied to particular hulls (i.e. hull 105 always is the Alchemy ship). PHost 3.x allowed you to make these race-dependent (i.e. small freighters only hyperjump when owned by the Rebels). PHost 4 goes a step further and allows to define these things separately for each ship.
If enabled (AssignTo=Ship in hullfunc.txt), this allows some more realistic play: when you capture a Rebel ship, it will hyperjump for you, too, and when Rebels capture a small freighter you built, it will not jump. In addition, it makes possible an add-on that allows you to buy additional capabilities for your ship.
There are now a number of new functions which need the possibility to assign properties to individual ships: ships can be CloneOnce (and get Unclonable when cloned), likewise GiveOnce and Ungiveable. This can be used to make ships more valuable, and to implement additional rules (i.e. "you can't trade ships that are heavier than 400 kt"). There is now also a Level2Tow which makes your ship stronger when towing.
(4.0i) PHost 4.0i added another boatload of hull functions. There are now smaller versions of the Chunneling ability, namely ChunnelSelf, ChunnelOthers, and ChunnelTarget. Some old ship abilities can now explicitly be assigned explicitly, to give you more flexibility: Tow, PlanetImmunity, Boarding. You can now give these abilities to any race, and also tie them to ships (e.g. Klingon-made SDSFs are immune against planet attacks). There is a new terraforming function, and a few new defensive and combat features (AntiCloakImmunity, FullWeaponry, HardenedEngines, HardenedCloak, IonShield, Commander). The list ends with a Repair ship, and an Academy ship for the new experience system.