Not an essential item, but refuelling manually can become a bit of a chore on large ships like the panther clipper
Travelling too fast through a planet's atmosphere without this will damage a ship. It is possible to land and take off from planets by travelling very slowly and using time advance. But it is a lot easier to buy atmosperic shielding.
Cargo Bay Life Support
Essential for transporting slaves or live animals. Flying through space without it will turn slaves into fertiliser and live animals into animal meat. In both cases this is a major financial loss. Economists might argue that animal meat should be more expensive than the live animals they come from but not in this game.
Extra Passenger Cabin
Required for transporting people around. They take up quite a bit of space, so it is not recommended to have them unless you are running a taxi business.
Flying through the atmosphere of a gas giant with this item allows you to scoop fuel. Hydrogen fuel is very cheap, so this is only useful for travelling to distant worlds and setting up mining machines.
Cargo Scoop Conversion
Allows you scoop up goods floating in space. Somewhat redundant in First Encounters as the Tractor Beam Cargo Scoop does the same job and occupies less cargo space.
Tractor Beam Cargo Scoop
Scoops up goods like the cargo scoop conversion but does not require a fuel scoop. Essential for mining asteroids and can be used to pick up cargo after a battle. Unfortunately this can be rather tiresome so many players will not bother.
MB4 Mining Machine
Essential tool for the side hobby of mining planets.