Nimbus by Alia covers the mythology of souls/Spike's soul, set from around Harsh Light of Day. It isn't online but I have a copy I was given only last week if you want to pm me.

Future Sins Past by dreamsofspike
Takes place in an AU where things went a little differently at the end of "What's My Line", and the Initiative came to town a bit earlier than in canon. Spike is not paralyzed in the church that night, but his unlife is still irrevocably changed. In a misguided attempt to restore her childe, Drusilla performs a spell that goes terribly wrong, and will change the course of not only Spike's life, but the Slayer's as well, forever.bloodshedverse . com/stories.php?go=chapters&no=7458
Lets get lost by herself
Set immediately post-season 2. Buffy's run all the way to NY, and encounters a Spike who feels he's made a bad bargain.nocturnal-light . net/fanfiction/story/374/Lets_Get_Lost
Victims of Fate by ya_lublyu_tebya
Goes AU during 'Becoming'. The soul restoration spell has further-reaching consequences than anyone could have predicted, changing Buffy's life forever. And when her life begins to fall apart around her, she finds understanding in the last place she would have looked.spikeluver . com/SpuffyRealm/viewstory.php?sid=31210