Johnny English (Rowan Atkinson) carries a Beretta 92FS Inox as his sidearm throughout the film. In the opening montage, after he becomes a field agent, two guns (the Beretta 92FS Inox and a Walther PPK) can be seen on a table for him to choose. English grabs the Beretta and poses with it in front of a mirror, and subsequently carries it for the remainder of the film, although every time he tries to use the gun, something goes wrong.
Note: The Beretta is never successfully fired throughout the film. The first time English tries to use it he accidentally drops the magazine, the second time the slide falls off forward, which shouldn't happen, and the third time he tries to fire it, feces comes oozing out of the barrel (from the sewer pipe he was in), which is not technically possible. Also when the gun doesn't fire the third time English racks the slide a few times, not sure what the problem is, but no rounds eject from the gun, meaning it's not even loaded. Oddly the slide doesn't lock back either, so the slide catch must not work either.
Glock 17
English's "sidekick" Bough (Ben Miller) carries a Glock 17 as his sidearm throughout the film. Bough's trigger discipline is excellent throughout the film, and he is clearly the more competent one of the pair.
CZ 75 "Pre-B"
Dieter Klein (Steve Nicolson), Klaus Vendetta (Douglas McFerran) and the rest of Pascal Sauvage's (John Malkovich) thugs carry CZ 75 pistols as their sidearms. Vendetta can be seen wielding one during the attack on the Queen's residence, pointing his pistol at the Queen's dog. Bough (Ben Miller) can also be briefly seen holding one after disarming Klein.
Walther PPK
A stainless Walther PPK is seen on a table during the opening montage as one of Johnny English's (Rowan Atkinson) alternate choices for a sidearm. It is likely he picks the Beretta over the PPK to poke fun at the James Bond films. Pascal Sauvage (John Malkovich) also uses one at his coronation. It is later picked up by Pegasus (Tim Pigott-Smith).
One of Sauvage's thugs carries an IMI Uzi in the Queen's residence. Several other thugs, including Dieter Klein (Steve Nicolson), can also be seen wielding Uzis in Sauvage's castle.
Rifles
Heckler & Koch G36K
A pair of guards carry Heckler & Koch G36K assault rifles in the opening sequence. These weapons are rubber props as the flash-hiders are solid and there are no vent holes in the handguards. This is logical, since there was no need for blank-firing guns in this scene and the guards get hit in the face with them seconds later.
Norinco Type 56-2 (modified)
A modified Norinco Type 56-2 is carried by Klaus Vendetta during the crowning ceremony. He tries to use this rifle to eliminate English, but Lorna Campbell (Natalie Imbruglia) spoils his plan, and later picks it up. The triangular rivet pattern on the receiver and the characteristic side-folding stock allow to identify it as a Type 56-2. It appears to have a shortened gas system and an unusual plastic furniture, and also has a strange scope (no regulation drums) and scope mount on top of the receiver.
Other
Smoke Grenade
A smoke grenade can be seen thrown by either Klein or Vendetta when English and Bough stumble upon their hiding place after they've stolen the Crown Jewels.
Walther P99
A Walther P99 is seen in the special features menu and is listed as Lorna Campbell's (Natalie Imbruglia) weapon of choice, but it is never actually in the film itself. This is another reference to James Bond.