The supplemental material disc of the R1 special edition DVD of Magnolia has about 8 minutes of hidden outtake footage. To access it, you need to select the 'Color Bars' option and wait about twenty seconds.
After watching the documentary "That Moment" on the supplementary DVD, you can see a deleted scene. The scene involves Orlando Jones' character 'The Worm,' his son (who appears in Officer Jim and Linda's scenes), and an unidentified boy. In it, the young rapping boy, Dixon, rushes into a restaurant where his father is staying, and eventually pulls a gun on him. The gun appears to be Jim's lost gun. Perhaps the scene would have further explained how it was so mysteriously returned to Jim in the end of the film. In the documentary, the director seems to be having a tough time with the scene, perhaps explaining why it was cut.
In the script, there is an alternate storyline for Stanley. In it, instead of running to the school library where he reads the books about the geniuses, he runs away to a coffee shop. Also in the coffee shop are Dixon (the little boy who raps for Jim Curring) and the Worm (who is mentioned in the movie, both in the rap and during Marcie's interrogation). The Worm (who is Dixon's father) notices Stanley and motions for Dixon to leave. At this point, Dixon finds Linda passed out in her car. In the coffee shop, the Worm and Stanley talk about their fathers and Stanley offers to give the Worm the money he won on the game show. The frogs begin to fall from the sky as Dixon runs in, asks the Worm if he got the money from Stanley, then pulls a gun (the one which he stole from Jim Kurring) on Stanley, demanding his money. The Worm convinces Dixon to give the gun up. They leave the diner after the frogs fall, drive by Solomon and Solomon, and throw the gun from their speeding car, which lands by Jim and Donnie. From the DVD documentary, it seems like this scene was partially filmed and then PT Anderson decided to scrap it.