These would be planets that were controlled by NPC factions like the Crimson Blades, Sha'din, etc. They'd count as enemy-controlled, and would help to balance two major concerns of players:

1) 'Good' planets are all taken (they're not, but people think they are)
2) No one wants to lose their own good planets.

Basically, everyone wants to scan good planets, no one wants to lose them. NPC-owned planets could add some additional interest to planet-capturing by adding new dimensions to planets and possibly making run-of-the-mill planets more desirable.

An NPC-owned planet would have some level of defenses that had to be breached by invasion, just like normal. Although there might be unique varieties of NPC planets (Asteroid Base, for example), the majority would just be ordinary planets like Gas and Volcanic and such. Any unoccupied planet might have the chance to get claimed by NPC's. Once claimed, the planet might receive:

Permanent passive bonuses or planet effects
Unique structures
A cache of loot - claim the planet and receive an unknown reward of resources or items
A unique name

Faction NPC ships might even have a small chance of dropping an item that reveals a scan of an NPC-owned world. I'll emphasize again that faction worlds would mostly just be normal unoccupied worlds that have the NPC effects on them - they wouldn't necessarily be any better than a normal planet, but someone looking to use a Melter might be extra intrigued to find a Sha'din-owned Icy on their scans.

There might be different levels of defenses on the planets too - for example:

Silthion Infestation
Normal shields and mines equalling 3k planet defense
Permanent Effect: The planet gains Invasion Defense equal to 50% of its MAXIMUM population

Silthion Colony
Normal shields and mines equalling 6k planet defense
Permanent Effect: The planet gains Invasion Defense equal to 100% of its MAXIMUM population

Silthion Hive
Normal shields and mines equalling 9k planet defense
Permanent Effect: The planet gains Invasion Defense equal to 150% of its MAXIMUM population

+10

I can remember someone suggesting this before, but +1 all the same.

+1 would like to see this implented in the game

you could also introduce hacking npc's for rp and planets

+1
Great idea.