The All 4 One is the collective name for Jeanne's four signature guns, Bayonetta's enemy in the original Bayonetta game later ally in the second who appears in Ultimate 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.
Colt M1911A1
Naked Snake's Spirit depicts him with his iconic highly modified Colt M1911A1 with a silencer attached.
The Desert Eagle Mark XIX with a 10 inch barrel 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 cannot be used.
"Love is Blue"
The "Love is Blue" is the collective name of Bayonetta's main pistols from Bayonetta 2 (which takes inspiration from the Mauser C96) and 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 from 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.
Shansi Type 17
EVA from Metal Gear Solid 3 appears in the game as a Spirit with her Shansi Type 17 drawn.
"Tornado-6"
Enhancing Major Ocelot's Spirit by leveling it up to Level 99 will turn the Spirit into 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 an M16A2 style handguard and aftermarket sights. 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 the Spirit of Big Boss (or more specifically Venom Snake from Metal Gear Solid V), which is unlocked after you enhance the Spirit of Naked Snake upon reaching Level 99 with it and is also seen on a Smash Tag icon that uses the same vector for 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, which was a reference to Metal Gear Solid 3, is absent from this game.
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. The smoke that comes from the grenade seems to be yellow in-game although there is a possibility that this may be due to the lighting changing during Snake's Final Smash.
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, returns as Snake's side special.
RPG-7
The RPG-7 with a PGO-7 scope returns from Brawl as Snake's side smash.