Military helicopter

AWACS
AWACS stands for Airborne Warning and Attack System. It's basically a flying Radar Platform that can be used to communicate with other airborne aircraft. Jim Houseman was on board one when he ordered the destruction of Shadow Moses by nuclear weapons.

AV-88 Harrier II
Aircraft that is used to keep other aircraft from reaching Big Shell. Raiden manages to disable it using the Stinger Missile. However before it crashes into the Ocean, Ray catches it in it's mouth allowing Solidus and Vamp to escape.

AC-130H Spectre/MC-130 Combat Talon
There is some confusion over this aircraft as it's fully armed but it is called a combat talon which unarmed. Naked Snake was supposed to use it to transport himself and Sokolov out of Tselinoyarsk to a reconnaissance point, during the Virtuous Mission.

M-21
Mothership that carried the D-21 the area where Naked Snake was going to be deployed in Operation Snake Eater. based in the A-12 'Oxcart' that would later become SR-71 'BlackBird'.

D-21
Reconnaissance drone that flies over enemy airspace faster than any enemy aircraft or missiles that may be sent to intercept it. Naked Snake is deployed by one of these at the start of Operation Snake Eater becuase of the Migs that are in the area.

VVA-14 (WiG)
Ground effect vehicle that is used for transport. Snake and EVA use one to escape to Alaska from Tselinoyarsk

MIG-21 'fishbed'
Used to control the airspace over Tselinoyarsk. Snake avoids them with the D-21 and when him and EVA try to escape a couple of MiGs threaten to shoot them down but Nikita Khrushchev calls them off. In the battle with The Boss MiGs have been odered to bomb the area giving Naked Snake and The Boss a time limit for their battle.

Mi-24 Hind B/D
"B" prototypes (Identified by their "greenhouse" style canopies) are used by volgin to transport the Shagohod to Groznyj Grad. They patrol the mountainous areas and can be used to transport troops.

"D" type production models are featured in Metal Gear 2: Solid Snake and Metal Gear Solid in which Solid Snake must engage them (the Hind-D from the latter game notably being piloted by his brother Liquid Snake).

KA-60 Kasatka
Helicopter used by the Gurlukovich Mercenaries to land on both the U.S.S. Discovery and the Big Shell. Otacon uses one to carry the hostages back to shore from the Big Shell before it sinks.

Sikorsky SH-60 Seahawk
Helicopter used by the US Navy to transport the SEAL Teams to the Big Shell.

Cypher
Reconnaissance drones that act as flying surveillance cameras in outside Areas. Can be disabled temporarily with a Chaff grenade or can be shot down with a rifle or handgun. There is also an armed version with a machine gun.
 * These are used to guard the Oil Fence and Raiden must use the PSG-1 to destroy them.
 * At one point in the game a cypher has a C4 sensor above it's camera. which must be shot out before Raiden can proceed.
 * Snake uses a cypher for vertical recovery in Super Smash Bros. Brawl.

Flying Platform
Guards use these in areas where it's difficult to get to such as the canyon, up in the mountains and in the jungle. Provides greater mobility to the guards and provides a shield for them to hide behind. It often comes with a light which can be used to blind intruders as they attempt to target the pilot. However, its main weakness lies in its design: as it is a flying platform, the body of the pilot is exposed and therefore vulnerable to gunfire.