Flagship/Legends

A flagship was the primary command ship in a commander's fleet of ships, and usually the one that the commander was aboard.

The flagship of a starfleet's commander, such as Home One to the Alliance fleet in 3 ABY, was considered the flagship of the entire fleet.

Sith Empire (Jedi Civil War)

 * Leviathan - Darth Malak's flagship / Flagship of the Sith
 * Ravager - Darth Nihilus's flagship

Galactic Republic

 * Katana - Flagship of the Katana Fleet
 * Reliance
 * Sojourn - Admiral Carth Onasi's Flagship

Confederacy of Independent Systems

 * Invisible Hand - General Grievous' flagship / Flagship of the Confederate Navy

Trade Federation

 * Saak'ak

Centrality

 * Wennis

Xim the Despot's Empire

 * Queen of Ranroon

Hapes Consortium

 * Song of War - Isolder's flagship / Flagship of the Hapan Navy

Galactic Empire

 * Executrix - Moff Wilhuff Tarkin's flagship
 * Exactor - Darth Vader's flagship
 * Devastator - Lord Tion's flagship / Darth Vader's second flagship
 * Executor - Darth Vader's third flagship / Flagship of the Imperial Navy
 * Whelm - Flagship of the Azure Hammer Command in Sector Zero
 * Guardian - Fleet Admiral Gaen Drommel's flagship
 * Iron Fist - Warlord Zsinj's flagship
 * Lusankya - Ysanne Isard's flagship
 * Reaper - Grand Moff Ardus Kaine's flagship
 * Chimaera - Grand Admiral Thrawn's flagship / Flagship of the Imperial Navy
 * Eclipse - Resurrected Emperor Palpatine's flagship
 * Eclipse II - Resurrected Emperor Palpatine's second flagship

Imperial Remnant

 * Gorgon - Admiral Daala's flagship
 * Knight Hammer - Admiral Daala's second flagship
 * Emperor's Revenge - Carnor Jax's flagship
 * Chimaera - Admiral Gilad Pellaeon's flagship
 * Right to Rule - Grand Admiral Gilad Pellaeon's flagship

Rebel Alliance / New Republic / Galactic Federation of Free Alliances

 * ''Champion
 * Defiance - Admiral Ackbar's flagship / Flagship of the New Republic Fleet
 * Galactic Voyager - Admiral Ackbar's flagship / Flagship of the New Republic Defense Fleet
 * Home One - Admiral Ackbar's flagship / Flagship of the Rebel Alliance Fleet / New Republic Defense Fleet
 * Megador Admiral Gilad Pellaeon's flagship / Flagship of the Galactic Alliance Defense Fleet
 * Poesy
 * Pride of Selonia
 * Ralroost Admiral Traest Kre'fey's flagship / Flagship of the Galactic Alliance Defense Fleet

Ssi-ruuvi Imperium

 * Shriwirr

Yuuzhan Vong

 * Blood Sacrifice
 * Kur-hashan - B'shith Vorrik's flagship
 * Sunulok - Warmaster Tsavong Lah's flagship
 * Yammka - Supreme Commander Nas Choka's flagship
 * Yammka's Mount