Humans Spider-Man Has Killed
ASM Annual #5 Deliberately killed the Finisher by returning a fired missile back to his tank.
Amazing Spider-Man #121 Accidentally killed Gwen Stacy, snapping her neck while she fell towards her death, thrown by Norman Osborn. It was a lose-lose scenario, so Norman gets the credit for the kill.
Marvel Team-Up #31 Killed Drom the Backwards Man. Spidey and Iron fist take on Drom, and smash his mirror on him. This causes Drom to rapidly reverse-age into nothing, effectively killing him. In the narration, Spidey regrets doing this.
Spider-Man vs. Wolverine #1 Accidentally killed Charlemagne (Charlie). She committed suicide by attacking Spider-Man during his fight with Wolverine.
Web of Spider-Man #91 Kills Whisper-3, member of the Foreigner's Death Squad. Uses Whisper-3 to block Pulse-2's energy attack. Pulse-2 then aborted the mission and commited suicide. Note that the Death Squad was founded on the assumption that the agents were expendable, and would be replaced, e.g. by Whisper-3 and Pulse-3. Even so, Spidey could have simply dodged the energy blast, and showed no remorse for the death.
Ultimate MTU #1 Spidey plasters webbing all over the face of an bystander who makes an anti-mutant comment. The webbing is clearly sufficient to suffocate them. To be fair, I suspect that this is simply a scripting mistake, or else that Spidey deliberately created not-very-sticky webbing, or some other reason why this one shouldn't really be counted.
Amazing Spider-Man Vol.2 #42 Apparently killed Shade while in the Astral Plane, by tossing him against his own energy-storage cocoon, hoping to cause a loophole.
Amazing Spider-Man Vol.2 #50 Accidentally killed two members of the Latverian Liberation Front. Diverted a missile shot by one of their partners to the only place it wouldn't cause any casualties, a hole in the ceiling. Unbeknownst to him, the two guys were arriving to join the fray, and decided to use the hole to enter. Lose-lose scenario, not his fault.