Spirit cults are an easy way to give players access to Rune spells that they cannot normally get from their local cults. For example, if the players (a bunch of Lightbringers cultists) want access to Fear, but Zorak Zoran is not surprisingly unappealing, create a spirit cult like the Death Maidens, the spirits who herald the coming of Death.
Or lets say we want access to Truespeak but none are interested in Lhankor Mhy – then the Old Woman spirit cult can provide it!
Spirit cults are also a way to provide limited access to another god. Sure there is not a lot of Orlanth Thunderous worship in Karasal satrapy, but there might be a little spirit cult of the summer Thunderstorm that provides Cloud Call.
In general, spirit cults provide between one and three special Rune spells. A few provide more (like some Common Rune spells), but the overwhelming majority just provide a single special Rune spell. Most are something supplemental to the existing local religion – they support activities that are not important enough to support a full-fledged cult of hundreds of dedicated initiates.
I tend to lump all sorts in localised little cults under the spirit cult header. Clan wyters, city gods, local nature spirits, old heroes, etc.