Jules (Samuel L. Jackson) carries a 9mm Star Model B throughout the film. Some audiences have been confused due to the Model B's visual similarity to the .45 ACP M1911 (like Vincent's Auto Ordnance 1911) and some movie critics have (wrongly) listed Jule's reference to his gun as "Mr. 9mm" as a goof, but as the Star Model B is a 9mm gun, it is not a mistake.
When Butch Coolidge (Bruce Willis) returns to his apartment to retrieve his father's watch he finds a suppressed MAC-10 in 9 mm on his kitchen counter and uses it to kill Vincent (John Travolta) as he comes out of the bathroom. According to IMDb, the MAC-10 belonged to Marsellus Wallace, who left it on the kitchen counter while going out to get himself and Vincent some breakfast.
Smith & Wesson 4506
After Butch runs over Marsellus Wallace (Ving Rhames) with his car and is subsequently hit by another car, Marsellus gets up, injured, and fires at Butch with a Smith & Wesson 4506 (with adjustable sights and sight guard), hitting a bystander. Marsellus chases Butch into Maynard's pawn shop. Butch attacks and manages to disarm him and takes the 4506, but before he can shoot Marsellus, Maynard (Duane Whitaker) captures them at gunpoint, taking the 4506 for him and Zed (Peter Greene).
Remington 870
Maynard (Duane Whitaker) captures Marsellus Wallace and Butch Coolidge with a Remington 870 with an extended magazine tube.
Taurus Model 689
After Brett and Roger are killed by Jules and Vincent, a character known only as "Man #4" (Alexis Arquette) bursts out of the bathroom with a .357 Magnum Taurus Model 689 with a custom ported barrel, and fires six shots at them. Despite the close range, neither Jules nor Vincent are hurt and they kill Man #4. Afterwards, they remark on the size of the man's "hand cannon" and Jules comes to believe that God deflected the bullets. (Thanks to Phoenixent, who confirmed that the revolver was a Taurus Model 689.)