Codename

Boss
Boss was a title given to Americas greatest soldier. The Boss gained the title due to her achievements in WWII. Naked Snake gained the title Big Boss after defeating The Boss. Liquid was also called boss. Solidus at one point describes himself as the boss around here.

Snake
codename given to Naked Snake and his subsequent sons. Raiden was given this title briefly due to Solidus being his adoptive father.

Solid Snake and Liquid Snake were given their names as they were opposites to one another. Solidus was given his name due to him being the perfect mix of the other two.

Fox
This was the codename given to the greatest soldier in Foxhound.

Adam and Eva
Originally the codenames of two NSA codebreakers that defected to the Soviet Union. They were supposed to meet with Snake to help him on his mission. However neither of them show up allowing a Chinese Spy to use the Eva codename to fool Snake. It is later revealed that Ocelot is Adam.

Ocelot
Variations of this were used by Revolver Ocelot such as Major Ocelot and Liquid Ocelot.

Rat Patrol 01
name of a group sent in to investigate Ocelots Insurrection. It is later pointed out by drebin that the letters can be rearranged to spell out Patriot showing that they were really sent by The Patriots.