I've given thought to just this sort of thing over the past few years. Some of these are (at least tangentially) at Midian's core.
While I have avoided (intentionally) the True Nature of an immortal soul--leaving that the sole province of the setting's religions--there is some remnant spark that sometimes remains after death. This can be anything from a raw energy used to power some magics, to phantoms little more than imprinted scenes of the past, endlessly repeating, to fully sentient spirits retaining all of their knowledge and personality from life. All of these various aspects can prove useful in the game.
A necromancer can use various means to force a spirit's compliance. This can range from magics that dominate a spirit into following your command, to more subtle arts like promising the sprit's release after capture in exchange for information. Some examples of these methods are with the Angkou spell, which creates a guardian for an area by burying someone alive, ensuring their return as an angry spirit, and binding them to the site. The spirit's rage does the rest. Also, a high-level necromancer can imprison the soul of someone that they slay. This allows the necromancer to bargain with the spirit for its release. Depending on the religious beliefs of the victim, this can be quite effective. A prime example is with followers of the Temple of Light. One of the basic tenets of that faith is that you are rewarded in the afterlife by joining--becoming "one"--with The Light. To the faithful, having your soul imprisoned by a necromancer is far worse than the death itself.
Some imprisoned spirits would gladly have the chance at a form of immortality as part of a magic item, rather than the nothingness of death. It's not nearly as good as still being alive, but it beats the alternative. Some spirits simply aren't given an option but to become a component in a magical craft. A powerful alchemist can take the pieces and traits she wants from a trapped soul (especially one sacrificed for this purpose) and place them inside a magical item. This can range from an essence of fire from an imprisoned elemental, to a fully sentient former mortal.
Sometimes a spirit can simply be cajoled into service. That is, a shaman using Spirit Charm essentially talks a spirit into an item. Any bargaining will be between the spirit and the shaman, and may simply be convincing the spirit to assist by wielding its power through the object. Other shamanistic magics, such as the Tribal Totem, allow the shaman to "win" the spirit's aid by defeating it in battle--either before or after it dies. For example, a bear may be hunted & slain for the purposes of this ritual, and its spirit--as part of a carved likeness--would repel predatory animals from the village.
It is also possible to secure the assistance of someone's spirit before they die. The Art of the Deal that MoonHunter coincidentally mentioned, allows a magically-binding contract to be entered. Any agreement that can be met by the various parties can still mystically bind them in the afterlife. Of course, someone may not know exactly what they are getting themselves into, but that's their own fault for not reading the small print.
Some spirits can be dealt with by even beginning characters, if they are clever enough. A ghost may be haunting an area because of a task left unfulfilled. Its cooperation may be gained if the pc's promise to aid it. Alternatively, a spirit can be trapped on the wrong side of certain protective circles (but keeping it there until the circle is completed is enough of a task in itself), gaining the spirit's help in exchange for its freedom.