Aside from Morlun, who obviously killed him. Electro has beaten Spidey a few times: one time he even had Spider-Man at his mercy and he had him BEG so that Electro would spare the lives of Spidey and innocent people. Another time during the Sin Eater Saga, the second Sin Eater saga I should say, Electro also beat Spidey. He didn't want to kill him, rather he left him alive to suffer defeat, but Spidey beat him two issues later. I think Electro won during Millers MK Spidey story as well. Who else beat Spidey? I don't think the Kingpin ever has, they've only fought in terms of physical combat about seven times total. The Hobgoblin once beat Spidey and the Kingpin had to save his life (Spidey's life, not the Hobgoblins.). Can anyone think of any other examples?
Freakin Trapster, or Paste-Pot-Pete if you prefer, beat Spidey back during the "Acts of Vengeance" - If I remember correctly, he totally outclassed him too. Though when he claimed to have killed Spidey, the think tank of Dr Doom, Wizard, Kingpin and others demanded to see a body. Trapster then went to the river to find it, little knowing that Spidey had somehow obtained cosmic powers. The rematch had Spidey whipping Trapster, but it was the fact that he was beaten at all in the manner he was that bothered me.
Uncanny X-Men 190-191 had Kulan Gath turn Manhattan medieval. Literally. Everyone except for Spidey. Spidey was captured by the medieval Avengers and then eventually tortured by Kulan Gath (he eventually died from the injuries) - Dr Strange sent time backward to erase the damage that KG did, which meant Spidey never died at all.
There's actually a lot of examples. Spidey is often beaten by opponents then has to figure out a way to defeat them in the rematch. But these two particular stories come to mind in answer to your post.