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?
Like Common-Sense, Tingling! said, Spidey's enemies often get early victories against him. He lost his first battles against Doctor Octopus back in ASM #3 and the Sandman in ASM #4. The Scorpion knocked the stuffing out of him in their first battle in ASM #20, before Spidey realized he couldn't win a slugfest and won their next battle by using his speed and Spider-Sense to dodge the Scorpion's blows. The second Vulture knocked out Spidey in their first battle in ASM #48 and left him for dead, though in that case Spidey was weakened by a flu virus. Spidey is particularly vulnerable to villains who use gas as a weapon; for example, the Kingpin in ASM #52 and subsequent issues, White Dragon in ASM #184, and Boomerang in SSM #144 or 145, all used gas to knock him out. (Given that Spidey has been able to prepare for battle by devising and wearing a gas filter, one must wonder why he doesn't just incorporate one into his costume regularly.) He's been knocked out at least couple of times by bullets grazing his head (the Red Skull's hoods in ASM Annual #5, Hammerhead in ASM #114). Hammerhead once knocked him out (around ASM #130) by head-butting him from behind. Norman Osborn -- while not in Goblin garb -- knocked him out with a punch to the back of his head in ASM #37. Kraven the Hunter paralyzed him temporarily with his electrolyte-magnetizing ray in ASM #47, and knocked him out (by what means I forget) in a Marvel Team-Up issue co-starring Tigra. During his first incarnation in the '70s, the Jackal, despite having no superhuman powers, won every battle he had with Spidey, knocking him out with two blows (without using his drugged claws) in ASM #139, then knocking him out with his drugged claws in ASM #148 and defeating him (when Spidey was still weakened from the last drugging) with claws, non-drugged, in ASM #149. Daredevil's not a villain, but he knocked Spidey out in PPTSSM #110 (the end of the first Sin-Eater storyline).
I seem to recall someone from Marvel saying that Spidey's losing so many battles made him a more realistic character than other comic book heroes (probably DC heroes, to be more specific). But that cuts both ways. It's not realistic for someone to win every battle, but on the other hand, it's not realistic for a supervillain to knock out his archnemesis and then not finish the job.