Just realized no one listed some of the older very best stories out there. You have probably read them but just in case you haven't here are the links:
Imitation of a Man ---- by: Darkapplehttp://www.livejournal.com/tools/memories.bml?user=darkapple&keyword=Imitation+of+a+M an&filter=allThe events of "Dead Things" plunge Buffy and Spike into Spike's human past in an
experience that transforms their relationship. The action begins with Buffy's return
to the police station alley where, minutes before, she left Spike beaten and bloody.
WORD COUNT: 327,649
The Butterfly Effect -----by cousinjeanhttp://dark-solace.org/elysian/viewstory.php?sid=421&warning=NC-17THIS IS THE VERY BEST SPUFFY STORY EVER.
Summary: Five months after the events of "Chosen," a still grieving Buffy must follow a time-travelling demon back to 1997 (circa Season 2) Sunnydale to prevent him from destroying the timeline--and try not to destroy it herself in the process.
DANCING LESSONS---by: COUSINJEAN and the Redemptionistashttp://community.livejournal.com/dl_archive/2005/08/13/This is a huge three book story. Continuity notes: This story begins immediately following the events of the Season 5 episode, "The Body." Spoilers for S5 follow, except for the episode "I Was Made To Love You." We're pretending that one never happened.
NORMAL AGAIN --- BY: RICHARD BACHMAN http://www.fanfiction.net/s/784245/1/Normal_Again it is also on the CRYPT site.
Instead of Buffy, Spike gets a dose of demonic goodness inserted into his system. As his consciousness is transported to an AU where he finds Sunnydale is no longer the good old Sunnyhell he despises and knows so well, things are getting a bit surreal for the poor bleached wonder.
WARNING: This fic is dark and ansty but I suppose that we kinda got used to it after watching whole bleedin S6.
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This is another long involved series with a very guilt ridden Spike.
THE OLD BLOOD SERIES --- by Nan DibbleOLD BLOODhttp://www.allaboutspike.com/fic.html?id=506While controlled by the First, Spike sired a number of fledgling vampires, something he'd specifically refused to do ever before. Recovered by Buffy from the First, Spike sets out, with Dawn's help, to assassinate those fledges, while assisting Buffy with training the SITs and trying to avoid resuming their destructive sexual patterns of Season 6.
Post-Showtime, Rated R, Spike & Dawn, Spike/Buffy, 57000 words.
BLOOD KINhttp://www.allaboutspike.com/fic.html?id=536Follows from Old Blood. Roving Turok-han are decimating Sunnydale's vamps. Willing to fight but needing a leader, the vamps fix on an unwilling Spike, who summons Angel�who's in a position to take over everything Spike cares about�to form a fighting partnership between Sunnydale's vampires and Buffy and the SITs. Also Dawn returns to her Key state and Spike attempts to recover her.
THE BLOOD IS LIFEhttp://www.allaboutspike.com/fic.html?id=740Follows directly from the end of Blood Kin. Now AU. The Hellmouth is shut, the First defeated. Spike, Buffy, Dawn, and the remaining SITs must deal with new challenges--Buffy, about her role as Slayer and partnership with Spike; Spike, about the horrible (to him) prospect of becoming a champion of the PTB and about whether to claim the role of the active Master Vampire of Sunnydale; Dawn, about whether and how to grow up and handle an intense but angsty romance (sort of) with vampire Michael. S/B, Spike-Dawn friendship. Rating R, chiefly for violence and profanity.
BLOOD RITEShttp://www.allaboutspike.com/fic.html?id=1020AU, continues from The Blood Is the Life. As Spike and Buffy try to hold onto their partnership and their love, recently unsouled Spike tries to secure his position as self-proclaimed Master Vampire of Sunnydale...against the wishes of The Powers That Be and the Slayer's ancient mandate. Magic, new arrivals, old friends (and enemies), dreams, visions, e-Bay, tribute blood, and cookies all play a part in the tense give and take between vampire priorities and human necessities.
There may be another book in this series, I'm not sure, but I don't have the name or link.
When We Dance ----- by Pepperlandgirl http://www.nocturnal-light.net/fanfiction/story/178/1/When_We_DanceSummary: Spike returns to Sunnydale five years after he left to get his soul. Buffy's with Angel and he has a new love of his own---but some things never change. And oh yeah, the world's ending (again).
HERE IS GONE ---- by: TERRI BOTTAhttp://dark-solace.org/elysian/viewstory.php?sid=1063Spike gets a chance to do a few things over again.
Forward to Time Past ------by Unbridled Brunettehttp://spikeluver.com/SpuffyRealm/viewstory.php?sid=23957Summary: The victim of a spell gone awry, Buffy finds herself trapped in Victorian London, where she meets a man surprisingly familiar to her.
THOUGHT YOU SHOULD KNOW ----by: ANGEARIA---this is a WIP with over 100,000 words
http://angearia.livejournal.com/53356.htmlSpike writes a letter to Buffy before the final battle in Not Fade Away. What happens when Buffy finally discovers Spike is back from the great beyond?