I think these all fit your criteria, although they are often quite different from each other.
The Bittersweets Series should be read in order but you can also read each fic alone if you don't want to tackle the whole thing. It's probably my favorite series in all spuffydom. There are several stories within the series that meet your criteria, most notably Forsake Me Not, Mrs Grieves and the Abandoned Husband, A Nice Place to Visit, But and Where They Have To Take You In.
The Bittersweets Series by Herself
Summary: An ongoing series of Spike/Buffy tales, meant to be read in order. The first springs from "Wrecked" in season six; the series veers off from canon at that point. These stories are het NC-17, with some slashy flashbacks.
There are four books in The Baby Series, and I think the final one, Down Comes Baby, fits your criteria. Possibly Book Three also. It's been a while since I read it so I don't exactly remember when things started going bad for them in this series, but definitely the last one has much misunderstanding and drama between the two of them as a married couple.
The Baby Series by Mrs Muir
Summary: Series of four epic fics covering the Babyverse. Spike is called away by Drusilla before he can meet Buffy at the Bronze in Tabula Rasa. He doesn't return to Sunnydale until after the fiasco of Xander and Anya's wedding. Things aren't the same as when he left town...especially Buffy. Post-Series, Season 6, Season 7
This is another of my favorite stories and it involves secrets between them as a married couple that are tearing them apart. Lots of good angst.
Sanctuary by MrsMuir
Summary: William Nagle and Alexander Harris have been best friends since the first day they met at Hyperion Preparatory School. Through the years they have always been there for each other. But one of them holds a deadly secret that will affect William's future with Buffy, the woman he loves. Will Buffy be able to hold onto the man she loves or will the secret rip them apart |