Every station or ship belongs to one of many factions, or groups. Most missions increase and/or lower the reputation with the various groups, as does destroying ships/stations/turrets from that group. Rescuing ships in distress (indicated by distress beacons when you get close to them) will also raise your reputation with the faction that ship belonged to. If your reputation with a particular group is too low, ships from that group will attack you on sight and you will not be allowed to dock at their stations.
If your reputation is neutral or better you can dock and trade at the standard stations. You can also go to one of the Guild stations and join them for a small fee; each guild has a unique set of ships and equipment, some of which is only allowed for purchase if your reputation is a high enough level. There is no limit to how many guilds you can join at once.