Doctor Octopus vs. Venom - One of Spider-Man's greatest enemies who has been Spider-Man vs. essentially an evil version of Spider-Man

Electro (in his original green and yellow costume) vs. Green Goblin (Norman)  - No reason other than the visuals. 

Fusion, the Twin Terror vs. Mud-Thing- This possibly crosses the line on the one-on-one, no other characters mentioned rule, but for a short time there, Hydro-Man and Sandman were fused together into one monstrous, wet, muddy form. For an even shorter period of time, Spidey fought a possibly-Firestorm-inspired menace, a pair of twins who'd worked at a reactor and been melded accidentally into one glowing being. I believe Spidey cured them at the end of the story, but hey, this is comics, so cures of this kind come and go. Two freaky, compound creatures battling it out to return to their original forms could make for a fun story. We could even round-robin the mixtures, leaving at one point, three of them co-joined and only one to stop them. "No Composite, No Return," maybe? "I've Got You Under My Skin?" "I Am So Into You?" "The Big Mix-Up?" We'll work on it... :-)

Green Goblin vs. The Vulture- The one would be an attempt to "up" the value of the Vulture as a Marvel villain, by pitting him in a cagey, merciless battle with a character who's always been fairly showy and respected and for a while there, held considerable cache. The story could open to find Norman Osborn once again on his way up, gaining considerable wealth and traction and Adrian Toomes watching from overhead, circling, knowing that Osborn has left himself vulnerable in some way he hasn't realized yet. We'd get to see Toomes as a cunning foe, far more intelligent and opportunistic than we've seen before, as he begins to exploit the weaknesses in Osborn's new undertaking, and ready to feed upon carcass of what Toomes will leave him holding. Of course, upon seeing the Vulture has taken an interest, Osborn's no dummy himself...