The All 4 One are the four signature guns of Jeanne, Bayonetta's enemy in the original game later ally in the second who appears in the game as a Spirit. These guns have traces of features from the Luger P08 evident in them. Despite having an alternate costume based on Jeanne, Bayonetta does not use the All 4 One pistols for she still keeps all fours of her Love is Blues instead.
The Desert Eagle Mark XIX with a 10 inch barrelled and a scope from Metal Gear Solid 4 is carried by Meryl Silverburgh's Spirit.
Heckler & Koch Mark 23
Much like during his previous appearance in Brawl, Snake keeps a Heckler & Koch Mark 23 in his holster but it is unusable.
"Love is Blue"
Bayonetta's main weapon the "Love is Blue" from Bayonetta 2 (which takes inspiration from the Mauser C96) is appropriately featured in her alternate costumes based on her appearance from that game and is used in a number of her attacks.
"Scarborough Fair"
The Scarborough Fair, highly based off of the Remington 1866 Derringer is the name of Bayonetta's signature pistols she uses in the first game in her eponymous series and are used in her alternate costumes that come from her appearance in it. In Super Smash Brothers, the difference between these and the Love is Blue are merely cosmetic and both weapons use the same attack animations.
"Tornado-6"
Enhancing Major Ocelot's Spirit by leveling it up to Level 99 will turn the Spirit into the Metal Gear Solid V: The Phantom Pain incarnation of Revolver Ocelot with his "Tornado-6" drawn. In Phantom Pain, the Tornado-6 is actually an altered Uragan-5 which in turn takes influence from Mateba series revolvers, while having the hexagonal cylinder design of the Chiappa Rhino series, and a break-action design similar to the MP-412 REX. Curiously, the Tornado-6 here seems to have a nickel finish in contrast to its appearance in Phantom Pain. The vector used by the Spirit is also used in an icon you can place on your Smash Tag as well.
Rifles
AR-15 Variant
Snake's Fighter Spirit, which is unlocked after you complete his Classic campaign for the first time, depicts him holding an AR-15 style rifle with a A2 handguard and a aftermarket rear sight. The angle the rifle is being held at makes it admittedly difficult for a more positive identification.
Blunderbuss
Newcomer King K. Rool's Neutral Special has him using a Blunderbuss with a comically oversized muzzle, the weapon being a callback to one of his moves in Donkey Kong Country 2: Diddy's Kong Quest. The Blunderbuss can not only fire cannonballs but can vacuum up either the cannonball or other opponents and shoot them back out.
"MRS-4"
The FAL-style "MRS-4" from Metal Gear Solid V is seen in a Smash Tag icon that depicts Venom Snake. The rifle in turn is influenced by the Beretta SCP-70/90, the Imbel MD 97, the FN FNC, the SR 88, the Daewoo K2, and the Gwinn Firearms Bushmaster Rifle.
The aforementioned Gekko Spirit/stage scenery also have Browning M2HBs mounted on them.
C4
C4 returns as Snake's down special, the only difference is this time it now has an obvious red light after being placed. The C4 shaped like a Butterfly (a reference to Metal Gear Solid 3) seems to be absent.
M18 Smoke Grenade
Snake uses an M18 smoke grenade to signal the beginning of his new Final Smash called Covering Fire, which signals a rocket barrage after Snake marks his location.
M224 Mortar
The M224 Mortar from Metal Gear Solid 4 returns as Snake's "Up Smash".
M67 Hand Grenade
The oversized M67 hand grenades from Brawl return as Snake's Neutral Special.
"Nikita Missile Launcher"
The "Nikita missile launcher" from Metal Gear Solid 2, which in turn resembles a FIM-92 Stinger launcher, returns as Snake's side-special.
RPG-7
The RPG-7 with a PGO-7 scope returns from Brawl as Snake's side smash.