Minor Plot hole: The Particle accelerator vaporizes Flint Marko's clothes,skin,organs and bones. But it decided to keep the cute locket intact.
Minor Plot hole: The Pumpkin bombs in the movie have different effects depending on what is needed for the story. They can be thrown at Harry's face to cause some facial scarring or they can be thrown at the Symbiote to completely vaporize organic beings. There is probably a ON/OFF button on the side to make the bombs useful or not.
Major Plot hole: Flint Marko tries to flee from policemen and falls in a Particle accelerator, 30 seconds before it is scheduled to move sand around. The scientists did notice a change in weight, but not the actual change in weight because that would make too much sense. In short, the amount of sand doubled and they thought it was a bird that would leave once the machine started. The scientists were also hurt by the recession since they could not buy actual cameras to see the experiment or actual fences to block retarded escapees to fall in their machine.
Major Plot hole: Spider-Man comes to the rescue of Gwen Stacey who is tangling off a building. Hundreds of people on the ground are killed/hurt by various falling wall and floor parts but they don't count because they are not hot blondes. Afterwards, when she is saved, Spider-Man leaves the scene even though the crane is still acting crazy and damaging new buildings and people.
Major Plot hole: Aunt May and Peter Parker learn at the police station that the actual killer of Uncle Ben is Flint Marko. The authorities knew this information since Marko was in prison (because he was arrested for that) but decided to inform the family during the third movie instead of the first one.
Major Plot hole: Eddie Brock goes to church and ask God to kill Peter Parker. Why? Because he proved Brock forged a false picture he submitted as a legit one and because he started dating a girl he met once. But both happened the same day so it's probably legitimate.
Major Plot hole: Venom captures Mary-Jane to set Spider-Man into a trap. That's good, although he met Parker when he and Mary-Jane were not together anymore and thus could not know the existence of their relationship. (Unless they were on Facebook).
Major Plot hole: Harry Osborne's butler informs him at the end of the movie that his father was not actually killed by Spider-Man but by his own glider. The butler knew this information since the end of the first movie but decided to keep his mouth shut until Harry almost died from his quest of avenging his father.
Major Plot hole: The final showdown of Spider-Man/Harry vs Sandman/Venom is widely popular around the country by being broadcast live on TV. The fight is so interesting that the NYPD or the SWAT or the US army does not want to get involved. A couple of snipers could have killed Venom.
Plot contrivance: When Flint Marko was transformed into Sandman, he received the obvious sand-powers of invulnerability, merging with random shit...and flying.
Plot contrivance: A small meteorite containing the dangerous Symbiote falls on Earth...just beside the only scooter on Earth owned by a spider-mutated man.
Plot contrivance: Peter Parker decides to get rid of his villainous Symbiote suit in a church. Why? Because Spider-Man 3 is a very religious movie with strong themes of faith, self-sacrifice and emo haircuts. It also happens that Eddie Brock is in the same church at the same time and that the church is completely empty. Everything is thus contrived to create Venom...who is killed too early to go to church himself.