Commander-in-Chief

A Commander-in-Chief (abbreviated CinC or CINC) is the supreme commander of an entire military force or at least a significant portion of the total force. The role is usually filled by an officer with the highest rank possible in the organization.

Starfleet
Starfleet's Commander-in-Chief was a position held by the senior Fleet Admiral, who took orders only from the Federation Council and its President. The post is also refered to as Commander, Starfleet. 

From the 2270 to the mid-2280s, the position was held by Fleet Admiral Heihachiro Nogura. He retired around 2285 and was replaced by Harry Morrow. ( novel: ;, , Star Trek: Pendragon)

In 2293, Fleet Admiral William Smillie was the C-in-C. Though he was not involved in Admiral Cartwright's conspiracy, he nonetheless resigned in shame after the Khitomer Conference, and was succeeded by Androvar Drake. Unfortunately, Drake himself had been a member of the conspiracy, and his actions as C-in-C nearly led to a war between the Klingons, Romulans and the Federation before his death at Chal. ( novels: ; ; Star Trek: Pendragon'')

Margaret Sinclair-Alexander served as C-in-C in the late 2290s.

By 2298, Admiral Nogura had been brought out of retirement to serve as commander in chief once again, and stabilize the upper echelons of Starfleet Command. ( novel: )

Mirror universe
In the mirror universe, Spock rose to the position of Commander-in-Chief sometime between the 2260s and the 2360s. 


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continuity
In, after the previous C-in-C resigned in 2372, Chief of Starfleet Operations Vice Admiral James Leyton was appointed acting Commander-in-Chief, giving him the opportunity to stage his military coup. (PDN: "Sword of Damocles")

Fleet Admiral James Cannon became commander in chief in 2377. (PDN: "True North")

continuity
In Star Trek: Remington, when the Federation established a full Federation military, the two new branches of the Federation military were given positions equivalent to the Commander in Chief: the Commandant of the Marine Corps and Chief of Staff of the Starfighter Corps.

Star Trek: Confederation continuity
In Star Trek: Confederation during the First Season the Commander in Chief was the Commanding Officer of the HMS Reliant and his orders were relayed to the Captain, and the Captain gave the General Order. ( "First Season") in Later Seasons the Commander in Chief had an office on Williams One and a personal small Starship the HMS Hinkley ( "Second Though Seventh Seasons")

The Commander in Chief is also the President of the Confederation of Earth and is also titled the "Prophet, Seer, and Revelator" of the Confederation, and he is the "Chief Presiding Officer" over Confederate General Confrence.

The United Federation of Planets Commander in Chief's roles belong to the Vice-Commander-in-Chief of the Confederation of Earth