To operate an interstellar starship you must have an Imperial Charter. Without a Charter you're operating in defiance of Imperial law - all ships must be registered and licensed. Even if you do not engage in actual piracy you can expect to be treated harshly if caught by the Imperial Navy or an Imperial Governor: Your ship will be confiscated and you'll go to jail for a very long time. It's the Office of Interstellar Transportation of the Adeptus Terra that formally issues most Charter types.

Limited Charter

This type of charter allows the holder and his ship to travel along a specific set of routes (or even along a single route), carry only certain cargoes, last only for a limited duration (either 1 or more hauls or a number of years), or otherwise operate under a set of limitations. Limited charters are often auctioned away to the highest bidder. Competition over charters can be fierce as they can mean the difference between continued operation or not for an independent captain. Examples include charters allowing limited trade with fringe worlds - carrying critical supplies to outlying colonies, hauling food relief for a starving hive, that sort of thing.

Hereditary Charter

Many charters are hereditary - they are tied to the ship, not the captain. When the current captain dies (or is otherwise removed from command) the new captain must present himself before the Office of Interstellar Transportation and swear and oath of allegiance to the Adeptus Terra. He will also have to fill out tons of paperwork, prove that he has the required skills required of a captain, and pay some heavy fees. But it's largely pro forma - the Adeptus Terra rarely interferes with the passing of hereditary charters. Although they are indefinite in duration hereditary charters are limited to certain ports of call, only certain cargoes or both. The trade cartels, transportation guilds and commercial dynasties try to hoard as many hereditary charters as possible.

Free Charter

Free charters are highly coveted, for they allow a captain and his vessel to roam freely across great tracts of space. Most free charters are linked to a specific sub-sector or sector, but some allow a free reign of an entire segmentum. Free charters do NOT, however, give the right to travel beyond the borders of the Imperium or engage activities such as trade with xenos.

Fleet Charters

A special subset of charters where the captain serves one of the Imperial battlefleets directly. Not very popular as they entail a certain level of risk, plus you have to obey the Navy chain of command (which can be quite antagonizing for a free captain).

Letters of Marque

A variant charter where the captain is empowered to fight the enemies of the Imperium. Issued where the the Imperial Navy doesn't have the resources or inclination to deal with all threats. Having a Letter of Marque allows a ship to be upgunned, beyond what is normally allowed for civilian vessels.

Warrants of Trade

Warrants of Trade are a special form of Free Charter, issued directly by the High Lords of Terra. In addition to the usual benefits of  a Free Charter they allow (even encourage) the captain to go beyond the borders of the Imperium. Out there he's pretty much empowered to whatever he likes - trade, diplomacy, or bloody conquest. He's even allowed to take back his plunder to the Imperium - as long as it's not outright heretical in nature he can trade in xenos goods, sell slaves, or pretty much broker any deal he likes. While inside the Imperium he must abide by the laws and regulations of the Imperium of course, but in practice his wealth and power allow him to get away with a lot of things lesser men can't.

Intrasystem trade

Intrasystem ships are the province of the local Governor; rules, fees and bribes will vary from system to system.