How do YOU want ghosts to be put to rest in your campaign? For example in many media there are established, common practices for ending a ghost's torment. Burying the bones, salting/burning the bones, or holding a séance to exorcise the ghost all leap to mind as a "standard" way in movies, books and TV shows.
If the GM wants to set a baseline... kind of a "try this first" sort of way to lay a ghost to rest, then it might be as simple as a Knowledge: Religion check. You can either give it a fixed DC or a scaling DC based on the TYPE of ghost and CR of the creature being faced.
If you want unique ghosts with unique removal options, Knowledge checks are still a good idea. Knowledge: Religion (DC 15) for example might reveal that while each ghost is unique, more often than not any site, object or person significant to the ghost while alive will carry some kind of clue or clues as to it's final rest.
As for getting clues to unique ghost exorcism, look again to your favorite media on such tales. Take the show Supernatural for example: say what you want about the show but they have a well-established ghost hunting/removal processes.
1. ghosts can't pass through a full barrier of salt - replace this with the spell Protection from Evil, sub in holy water, or even keep the salt thing
2. ghosts can be injured or temporarily dispersed by salt, holy water or iron - you could keep the first two, debatable if you change "iron" to "cold iron" for theatrical purposes
3. to exorcise a ghost, you need to salt and burn the remains of the person they once were - a good baseline, accessible with Knowledge: Religion DC 15 or 20
4. if no remains can be found, the ghost is bound to an object which must be destroyed in a similar fashion - again, a Knowledge: Religion check
5. certain ghosts, created in unique ways, fall outside of these parameters; these call for special means of removal such as exorcising a terrifying spirit that was born out of fear by forcing the spirit to confront the very fear that birthed it - in this episode the ghost caused a sickness; the sickness in turn generated clues to the spirit's unique nature
So imagine 4 PCs entering a haunted abbey. You know that the set-piece encounter of the adventure is confronting a CR 5 ghost and putting it to rest. The party is only APL 2 and the players are of average experience with RPG's and PF specifically.
Going in blind against a ghost is dangerous, perhaps even suicidal. If you're planning on just dropping this encounter on the PCs unprepared that's brutal. To this point let's hope that the players have SOME kind of forewarning as to the nature of the threat; old ghost stories surrounding the site (Knowledge: History, Local), reports from survivors showing signs of intense Fear effects and rapid aging (Knowledge: Religion and Heal checks); historical events of the site (Diplomacy/Gather Info, Knowledge: History).
So let's say, for the sake of argument, that the players know that they're facing a potential ghost in the ruins of the abbey. They will likely have an amount of holy water and perhaps spells at the ready so they can physically attack the ghost and defend against it. You, as the GM however, want the PCs to actually put the thing to rest, not just beat it in a fist fight. You have to communicate that to the players; you have to TELL them to treat this as something more than a dungeon with a monster to kill so they can loot it's treasure.
There are any number of ways to do this. If you have survivors of the ghost's attacks for example, they might describe how they went in confident in their holy water to defeat the ghost, they even used their weapons successfully, but somehow the creature came back. You could mention how, in histories of the haunting, many have claimed to have slain the ghost but it continues to infest the abbey. Whatever way you do it, subtle or not, the players need to be aware that JUST fighting the ghost isn't enough to end it's threat.
Now, let's presume that the players know that they have to defeat the ghost permanently, their characters have weapons to defend themselves and discorporate the apparition temporarily, AND they're willing to continue with the adventure. Now you have to show them what it takes to put the ghost to rest.
Haunts.
Room one: the charred nursery. PCs hear the sound of a wailing child. Entering the chamber they are suddenly in a scene - the abbess of the facility is desperately trying to soothe a baby. Despite her best efforts nothing she can do quiets the child. As she swaddles the baby girl, the child is staring into the fire over the nun's shoulder and suddenly its eyes glass over, it calms... and the flames in the hearth begins to grow... PCs have to avoid a Cause Fear effect as it seems like the fire is literally reaching for them
Room two: the choking dead. The smell of smoke permeates a chamber that had previously been bricked off. Once inside the room the PCs find themselves among several nuns led by the abbess, trying desperately to try and help a young girl calm herself. The room is lit by several candles on stands. The young girl is having some kind of fit or seizure on the floor of the room. Suddenly her eyes fix on the candles which all go out at once, filling the room with thick, black smoke. The PCs come out of it having to resist a Pyrotechnics spell effect even as 2 zombie nuns come at them through the haze.
Room three: the abess' regret. In an upstairs room the PCs smell scent of savory stew and a woman's voice: "here little one... I made you your favorite..." Investigating further the PCs are treated to a scene of the abbess emptying vial in secret into a bowl of stew and then delivering the food to the little girl. The two exchange pleasantries, the girl happily eating the stew until she begins to choke. Immediately the little one's eyes fill with sorrow turning to rage. The abbess begins to sputter, her skin appearing to boil even as she pleads for forgiveness. The PCs have to contend with some kind of Blistering Invective affect.
Room four: the mistaken apparition: back on the main floor the PCs encounter a Medium sized ghost hovering near the old kitchen ovens. The PCs may attack the creature who seems confused and upset. Through the entire fight the apparition won't stop crying. Upon defeating the creature (much more easily than they'd anticipated; this is important) the thing becomes much more defined; it is the old abbess. She laments poisoning the girl but exclaims her ward was evil through and through and begs for forgiveness. Finally, as she fades into nothingness she regrets not doing more for the girl's remains; "she deserved so much more than such caustic irony..."
Prior to arriving here the PCs should've found, in the other rooms, a book of last rites and burial procedures for interring a body in the mausoleum accessed through the cloister behind the kitchen; a hidden stock of dried herbs, all mentioned in the internment rite; the key to the mausoleum. Now in this chamber where the abbess' ghost was fought, in the ashes of the oven, the PCs find a set of bones and the twisted, melted remains of a locket they saw the girl wearing throughout all of the Haunt scenes.
The moment any of the PCs disturb the bones or locket a shriek of utter rage echoes from everywhere at once. All three of the ovens ignite (any PC/PCs within 5' of an oven needs to save or take damage) and a Small sized ghost begins to form, hissing that she'll live forever in the fire and never go into the "dark place!"
Final rest: PCs must inter the bones in the mausoleum. While trying to get there the party is confronted by a Small sized Ghost CR 5. This should be a tough but not impossible fight. Following the rite and interring the bones, both the abbess and the little girl materialize, embrace finally, the holy mother is forgiven by her charge and the two dissipate into motes of light.
