Here is a list, in sort of episode order, of places that I feel the Federation would have to guard, protect, or deny access to any species from visiting either for safety reasons or to protect the discoveries that a certain visiting starship uncovered:
- Talos 4
- The galactic barrier. I would think all races would be sending their ESP experts to the Barrier to get some silver contact lenses and become a god. It would have to be prevented unless the Feds are sending people there too. Which I bet they are.
- anywhere near Charlie Evans
- the planet with the ore that splits you into 2 people in the transporter
- both Dr Korbys planet and Mudd, rogue android warning
- Miri's duplicate earth, bio-hazzard alert
- the border with the First Federation, maybe Balok is not done testing yet
- the Shore Leave planet. How long before somebody has the "random" thought to kill everyone on the planet?
- Trelane's area of space. If Trelane taught someone how to make his machine, wouldn't they be as dangerous as someone who had spent time on Talos 4?
- near the Gorn border, Cestus 3 area
- Landru's society as well as Sigma Iotia, Gamma Trianguli 6, Capella 4, Omega, Neural: cultural contamination repair in effect, or cultural contamination continuing depending on your point of view.
- Zeon and Ekos, seriously do you think humans would ever be safe or welcome there again after John Gills help and assistance?
- Ceti Alpha 5. No wait, 6. No wait, 5. Whatever.
- Is it safe to go to Emeniar now or did they just switch to a real war that needs to be kept away from?
- The Spore planet, because in the 23rd century happiness is something you take a phaser to, only hardship is good for the species.
- The Organian homworld. If in fact they were actually ever there, they clearly did not want anybody returning.
- Lazarus home world. Would you ever take the chance that there wasn't something else hidden there that could reopen the portal and let the Lazarii back out?
- The Guardian of Forever. Wow, talk about something needing to be behind a rope. You can change history with it, alter timelines, go back and invest in Microsoft in 1980 and take over the planet. Hopefully a whole fleet of ships protects that place.
- Anyplace still inhabited by the flying Perogies after Deneva, Its unlikely those things moved en masse from one colony to the next but rather spread out along the way between colonies. They might even be fairly common in some areas.
- Apollos homeworld. Could you ever be sure the "gods" were gone, maybe there was more than just his temple at work there and he could return to try and get another ship. At least that god knew what he wanted with a starship. Laurels, bitch!
- How many systems did Nomad destroy? Were there any survivors and did they also figure out Nomads origins? Are Humans wanted for crimes against entire species in some parts of the galaxy?
- Halka was just the first time the Mirror universe was encountered, there was nothing specific about the place itself so it may not be guarded. However, after Halka, would there not be mass response to any incursion by Mirror universe forces appearing in the "real" universe? I think Starfleet would view Mirror Starfleet as being as big a threat as any Romulan just appearing in front of them.
- Was there just one Companion or do they wander that area of space kidnapping people to take care of?
- Any planet in the path of the comet with ability to age people
- The home of the vampire cloud creatures, and anyplace along their migration routes or spawning grounds
- Sargons world, there must be endless tech there its best nobody finds
- The Roman planet, now there is a group that would do absolutely anything to get advanced tech, that whole system must be under wraps
- Sigma Draconis, the Great Teacher could be very useful or dangerous. As could the library of the Fabrini on Yonada.
- The Gorgan is still in that cave, and can still be summoned by anybodys kids at a distance
- The Tholian border, not a fun bunch, and the area of spatial interphase where travelers can lose their ship or their marbles
- Parmen's group as they are dangerous and because humans can also learn the power. I bet it replaced Argelius a haven for sex tours though.
- Gideon is clearly a place with some issues, though they did keep the Emenian disintegration booth industry going after the war.
- Any more Kalandin outposts that are still guarded by their computers
- Mr Flints planet. There is a man who knows all the secrets of the species, would we demand he tell us all he knows or would he demand that we stay away?
- The rock creatures that created Lincoln will presumably keep doing that
- There is a machine that can swap the minds of a person into another body, male to female even. And get Shatner to buff his nails on screen. I think that would be guarded or dismantled.