What Could Have Been: The Vulture (who would've been played by Ben Kingsley) was originally going to be one of the main villains and would play the Final Boss role that Venom ended up playing. He was ultimately decided against since his role had no meaningful personal connection to the hero at all: he was merely Flint Marko's cellmate who hated Spider-Man for putting him in jail to begin with.
Neither Venom nor Gwen Stacy were present in the original planning packet, with a random woman serving the role Gwen later took.
Also, Gwen was originally going to be kidnapped for the final battle, not Mary Jane; Mary Jane would have talked sense into Harry instead of Harry's butler. A line Mary Jane said for this scene was actually used in the trailer: "We've all done terrible things to each other, but we have to learn to forgive each other or else everything we ever were will have meant nothing."
A scene with Eddie Brock coming to the Stacy's front porch and begging Gwen to take him back was actually filmed but not included in the final version, mainly since it connects with Gwen being the kidnap victim in the end, which was cut.
An entire character, a doctor whom Marko strongarms into helping find a cure for his daughter, ends up on the cutting room floor, even though he had evidently filmed several scenes. Ouch!
The scene where Marko meets Eddie was quite different from the "90's Batman" villain team-up that was shown. After seeing Flint pretending to be sand in a park's playground for his little girl to play on, Eddie comes up and talks to him, and convinces him that his girl may be cured yet, and he will help him get the cash if Flint helps him take on Spider-Man. Images of this park scene being filmed actually exist. This, followed by him learning from his daughter that she is irrevocably sick and just wants to die with her dad a good man, makes his Heel-Face Turn at the end, and Peter forgiving him, much more credible and poignant.
These scenes most likely were considered, at least somewhere along the line - they were, after all, used in the Peter David novelisation in lieu of what the movie actually gave us. Though the novelisation presents Peter and Flint making amends partway through the battle, while the film shows it after Venom is defeated, and it's really up to the audience to decide which is better (since stopping a big climactic action sequence so that characters to clear things up is pretty hard to pull off in a film). Both exist in some form, at least.
It is also rumored that John Jameson was originally to have an appearance, unknowingly bringing the symbiote back from his astronaut mission like he has in two otheradaptations.