1-Border Guard Station
The captain of this border station and most of those under him are both deeply racist and deeply corrupt. They harass any travelers that are not both human and white, plant illegal substances and weapons on innocent people, and also take bribes to let people smuggle, and that includes turning a blind eye to trafficking in sex slaves. Being out of the way, they have very lax supervision from on high, which is perhaps what turned them to the dark side in the first place. The PCs can be investigating the station or just be trying to pass through and get picked on.
If a mental hospital, all manner of things can be happening here, from sane people illegally imprisoned with the genuinely insane, to vile experiments being carried out upon the helpless patients, to the illegal creation of Deaders4502 and other undead. But hospitals with physically ill patients can have evil too, from thieves that prey on the injured, to an evil or insane doctor that is secretly making a new plague or a Frankenstein's Monster with the body parts of dead patients. The PCs can be looking for someone, or one of them is injured and has ended up here to be healed.
What better place for evil to take root then a prison? Many of the prisoners are no doubt evil to begin with, and often the staff meet evil with evil and thus become evil too.It could be that some criminals have an arrangement with the governor and some staff members;they are secretly set free at certain times to commit crimes and share what they have stolen with the prison staff in exchange for a foolproof alibi. The PCs can be investigating the prison, trying to bust someone out,who may or may not be guilty, or banged up themselves and trying to escape.
Whilst the majority of law enforcement are honest and are trying to do the right thing, there are plenty of them willing to take bribes, plant evidence, torture suspects if they can get away with it, even murder people. The PCs could be trying to rescue someone from the police station, or under investigation themselves, or trying to uncover corrupt police officers whilst undercover. Or perhaps they are being interrogated by good honest officers-they can fight their way out and become outlaws or try and get out legally.
There is perhaps no more likely a place to find evil then here. From the planning of wars on false pretenses, to planning to take over people's land unfairly, to being hand in glove with organized crime gangs, and much more. The PCs are most likely to be spies or assassins trying to infiltrate the place and either uncover evidence of wrongdoing or outright assassinate the wrongdoer.
Perhaps the villain here wants to bombard his home planet with deadly plagues aka Moonraker. Or the PCs are on it when it is attacked by space pirates and must fight for their lives. Or the villain is not an organic being at all but a computer like HAL that has gone rogue and is trying to kill the PC crew.
Many forms of evil can lurk in small villages, from cults that sacrifice people like in the "Wicker Man" film, to villages of deadly Xarloccians who murder those just passing through, to villages that are terrified by bandits. Or the PCs can be Customs Men/Women and the bad guys are occasionally violent smugglers that are supported wholeheartedly by most of the tax-dodging villagers who just want to buy cheap goods. If the smugglers only use violence to defend themselves and to punish informers, and if what they are smuggling is not dangerous drugs or slaves but things that the average villager wants and can buy from them, then most villagers will have good reason to see the interfereing PCs as the *bad guys*.
You can find all sorts of nasties in caves...mighty dragons, giant centipedes, bears, gangs of brigands, drow or the equivilant, perhaps even your world's version of Bin Laden. Again, in many cases they would not do harm if left alone, such as the bears and perhaps even the drow and are just defending themselves from the intruder PCs.
From body-snatchers, to Undead of various types and the necromancers who raise them, to vampires and ghouls, the PCs will find plenty of evil to fight. They could be ambushing those up to no good, or could be merely passing through certain graveyards when the earth cracks open and an entire graveyard of rotting Undead whales on them.
As long as there have been places of beauty set aside as National Parks for soceity to emjoy, there have been vandals, poachers and illegal land developers trying to ruin said beautiful places. The PCs could be rangers trying to protect the geysers and the wildlife from the thoughtless, the stupid and the destructive. Or they could just be passing through when they see something like that happen and have to decide if they will get involved or if they just don't care.
Orphanages have never enjoyed a good press and several of them are genuinely badly run, although most are not as hellish as the Taikan Solon Memorial Orphanage. The PCs could be trying to find an orpham who knows something about their quest, or perhaps they are orphans trying to escape from the place.
Perhaps the school is infested with bullies or worse who are preying on the good pupils, or perhaps it is well run but it is what is taught that is wrong. Or the school is in a Beslan-like situation and the PCs are the rescue team.
13-On A Ship
From band of sea-roving pirates to people plotting mutiny there is plenty of skullduggery to be found at sea. Or perhaps the PCs have been kiddnapped by a press gang and forced to serve upon the vessel.
Many of those rich enough to own private islands are crime bosses in their own right, and there are those who want to organize illegal human hunts on their own island. The PCs could be assassins, bounty hunters or members of law enforcement come to extradite someone, or could be just trying to stay alive and escape from the island.
Perhaps someone important has gone missing within it, either kiddnapped and in need of rescue or outright murdered, or an imprtant crime boss has made it his home and uses it to plot his crimes inside. Or it could be inhabited by a cult that is fond of human sacrafice or other such dastardly deeds.
Additional Ideas (4)
Cruelty to animals easily becomes cruelty to humans. If the area is a wildlife refuge poaching, waste dumping, and smuggling could be common problems allowed by lax rangers. More sinister is the individual who takes in homeless pets for sale to science laboratories or just tortured for 'fun'. It is possible for escaped pets to wind up in the hands of such monsters much to the tears of their owners.
An abandoned warehouse is an easy place for a street gang to take over and use for things like cooking up drugs, hiding contraband, and staying hidden from warrants.
A variation on #17, a keep may have been abandoned when it wasn't worth defending or was emptied out via brigands. If land surrounding the keep becomes wild, it would be an excellent, easily defensible place for a band of brigands to keep their home and loot in. Until something nastier comes along, of course.
A international airport would make it easy to bring in supplies and troops without drawing unwanted attention and you can have a escape plane on stand by for a quick escape for when the authorities decide to stop by.