>>96136817Someone's already mentioned the Sensational Spider-Man Annual #1 by Fraction and Larroca. Sensational Spider-Man had some fantastic Spidey/MJ stories around that time - the Women of Spider-Man after the Unmasked storyline during Civil War had a solid MJ issue (#32, I believe). And #41 had a glimpse of their happily ever after (last issue before OMD).
Spider-Man Loves Mary Jane by Sean McKeever and Takeshi Miyazawa is glorious, though not quite as strong on Peter and MJ - more MJ and Spidey.
JMS's run was really good for the first three or four years on the relationship. When he did Sins Past (which I don't hate, but it doesn't really make me happy either), and then moved them all to the Avengers Tower in preparation for Civil War, it lost a lot of the great relationship stuff, but it still had its moments.