NPC Settlements are effectively run by the game itself and cannot be joined by Companies. Instead, all characters have equal access to NPC Settlements, which are more limited than Player Settlements. For example, NPC Settlements only offer up to level 8 training. The NPC Settlements in the game are:
Rotter's Hole is is unique in that it has no Thornguards. This means that characters of low reputation will not be killed by them when entering Rotter's Hole. Players with low reputation can train there (to level 8). They can also use the refining and crafting facilities safely.
This also means that Rotter's Hole is the only settlement where player vs player combat is possible without Thornguard interference.