Just off the top of my head...
The Norman Osborn ressurection... one of comic's WORST moments. He should have stayed buried in the ground. And the way they painted him out to be the one "responsible" for all of Peter's bad luck since ASM #121 was just ridiculous. To give one villain that much power over Spider-Man was ludicrous.
The Clone Saga itself was far too long... but the Spider-Man era AFTER the Clone Saga... forced stories trying to convince fans to come back and silly ideas like Chapter One and upgrading the originals Stan & Steve stories... stupid and quite unecessary.
The Byrne/Mackie relaunch which came off as VERY forced... bringing about the retcon of Aunt May's death and making her a silly old woman waiting for her next heart attack. At least this time, they're giving her a bit of a backbone and a life.
Too many lame and silly Venom/Carnage/symbiote stories...
The last 80 issues of Web of Spider-Man was such a weak run, I'm surprised it lasted as long as it did...
And that's just the top of my head... The Spider-Man books (with a few shining moments... Sacosa's Sensational being one example) have been terrible since the early 300's of ASM, and that includes OMD being right up there. When I think about it, it surprises me that Spidey fans were created at all during the last 25 years... when you consider the mediocre and lame stories (again, with a few exceptions).