Strike one--The 9/11 issue. Not because it should'nt have been made but because JMS used Spidey to basically spout the notion that the United States probably deserved what it got on September 11th because of the terrible mistakes committed in the past, implying that the terrorists actions were justifiable. To be fair, it did try to make an attempt at honoring the men and women who acted heroically that day.
Strike Two--Sins Past, more specifically part 4 where the actual revealation that Gwen slept with Norman Osborn because of his "personal magnetism" was revealed. Despite JMS claims it fit into continuity, there was no way it could have, and he had to essentially re-write long established characters and have them act out of character in order for the situation to work. Plus we got a lously Goblin knock-off and later the awful Sins Remembered arc.
Strike Three--The Other, and although that was a story by commitee, it not only confirmed that Peter was bitten by a magical spider, which means that regardless of the radiation, he would've recieved spider powers (and likewise contradicting the entire theme of the spider-totem subplot in that there are certain mysteries that make it appear that science and the spiritual do not always contradict each other--plus bringing up the whole idea again after he had already effectively ended it in the book of Ezekiel) but we got those awful stingers that just screamed "Wolverine rip-off."
I do not "hate" JMS at all; I just feel that, when it comes to Amazing Spider-Man, he has worn out his welcome, especially now since he's pretty much ran the whole new age, mystical spider-totem crap into the ground. In other words, "Strike Three! You're out, JMS!"