So now that we know what the deleted scenes on the DVD/Blu-Ray will be, I tried to make a list of scenes/alternate takes/single lines we've seen elsewhere (eg, trailers, etc.) or heard of in interviews, but won't be included with this release. (For full disclosure, if this list looks familiar, it's because I've posted it on another message board before.) I didn't include scenes that are on the DVD/Blu-Ray (obviously) or anything that was just a different background CGed for promos (eg. Peter revealing his costume overlooking the city in the trailer versus on the bridge).
-- The alternate take of the scene where Peter gives Connors the decay rate algorithm from the trailer, where he's writing it on a chalkboard in what's presumably a home office rather than on a piece of paper in the kitchen. We can probably assume it's in the same (missing) scene where Connors tells Peter that he can see his father in him.
-- Wherever the lines 'Ready to play God?' and 'If you want the truth (about your parents), Peter, come and get it' were from. Probably, from the looks of it, they were cut out of scenes we've already seen.
-- 'Too dangerous!' and Gwen turning to Peter to smile after the coach asks him if he wants to play football.
-- Peter on the floor of the school library with his mask off shouting at the Lizard/Connors to 'Stop it, stop it right now, this isn't you' or whatever the lines were. (Speaking of which, where was this even from? I've seen gifs of it, but never the actual clip.)
-- The doorman scene isn't included in the deleted scenes reel, though we've seen it, obviously. I'm guessing it could have been filmed just as a viral video and that's why it wasn't included, but who knows.
-- The second screen app had a pre-visualisation for a scene where Peter and Gwen order take-out for their clock tower date and swing by to grab it from the delivery guy on a street corner, but maybe it wasn't filmed in the end. There was some behind-the-scenes photo of them swinging right in front of the clock though.
-- The part in the trailers where Peter seems to be wandering with his headphones on (maybe I'm misremembering that) along the waterfront at sunrise/set.
-- Whatever scene that involved Billy Connors that was filmed at a house. May or may not be the scene from that audition tape/mentioned in an interview where Curt either gets mad at him or he tells him to go to his mother after Billy asks him what's wrong as he looks at himself in a mirror post-transformation.
-- More of the first-person perspective scenes where he's running along the rooftops.
-- Billy and Martha visiting Curt at the mental hospital in the end.
-- 'You're a wanted man, Peter Parker' and 'My father has 500 officers looking for you'/'500? That seems a bit excessive', followed by Gwen smiling at Peter.
Did I miss any? I feel like I have, but I'm not sure.