My very favorite Wish!verse story is
I Will Follow by Kari Mouke.
Summary: NC17. Spuffy. An AU story of the summer of season three. Inspired by The Wish - no Evil Willow visit in this universe.There's also
Dueling Hearts by Blood Faerie, which has the Spike from the Wish!verse AND the Spike from the regular verse. You can't beat two Spikes.
Summary: Doppelgangland, When the portal opens and Vamp Willow comes through, Spike comes through as well unknown to the Scoobies. So they put back Vamp Willow and close the portal without realizing it they still had a doppelganger hanging around. Spike comes back from South America only to find some wanker playing at being him and now Sunnydale has two Spikes!The last one that came to mind was
Wreckage by HollyDB, which is set in the Wish!verse but is just a short ficlet, so may not be what you're looking for.
Summary: Buffy mourns the loss of a comrade when a favorite enemy shows up to play.