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, because of this the flagship was usually the most powerful ship avalible in the fleet, such as a Super Star Destroyer.

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

 * Naga Sadow's Flagship - Naga Sadow's flagship / Flagship of the Sith Empire

Brotherhood of the Sith

 * Naga Sadow's Flagship - Exar Kun's flagship / Flagship of the Brotherhood

Sith Empire during the Jedi Civil War

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

Stark Commercial Combine

 * Raptor - Captain Zur's flagship / Flagship of the Stark Commercial Combine

Galactic Republic

 * Reliance - Flagship of the Republic fleet at the First Battle of Empress Teta
 * Sojourn - Admiral Carth Onasi's Flagship
 * Invincible - Flagship of Ranulph Tarkin's paramilitary
 * Katana - Flagship of the Katana Fleet
 * Integrity - Flagship of the Open Circle Fleet''
 * Mersel Kebir - Flagship of the Rendili Home Defense Fleet

Confederacy of Independent Systems

 * Invisible Hand - General Grievous' flagship / Flagship of the Confederate Navy
 * Mersel Kebir - Flagship of the Rendili Home Defense Fleet

Trade Federation

 * Saak'ak - Trade Federation Viceroy Nute Gunray's flagship

Centrality

 * Wennis - Rokur Gepta's flagship / Flagship of the Centrality

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 Death Squadron / 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
 * Intimidator - Flagship of the Black Sword Command
 * 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

 * Vengeance - Inquisitorius Jerec's flagship
 * Gorgon - Admiral Daala's flagship / Flagship of the Maw Installation
 * Reckoning - Admiral Delak Krennel's flagship
 * Shockwave - Warlord Harrsk's flagship
 * Knight Hammer - Admiral Daala's second flagship
 * Emperor's Revenge - Carnor Jax's flagship
 * Relentless - Moff Disra's flagship / Grand Admiral Thrawn (impersonated by Flim)'s flagship
 * Chimaera - Grand Admiral Gilad Pellaeon's flagship / Flagship of the Imperial Navy
 * Right to Rule - Grand Admiral Gilad Pellaeon's flagship

Rebel Alliance / New Republic / Galactic Federation of Free Alliances

 * Home One - Admiral Ackbar's flagship / Flagship of the Rebel Alliance Fleet / New Republic Defense Fleet
 * Mon Remonda - General Han Solo's flagship / Flagship of the Solo Fleet
 * Defiance - Admiral Ackbar's flagship / Flagship of the New Republic Fleet
 * Galactic Voyager - Admiral Ackbar's flagship / Flagship of the New Republic Defense Fleet
 * Intrepid - General Etahn A'baht's flagship / Flagship of the New Republic Fifth Battle Group
 * Peregrine - General Garm Bel Iblis' flagship
 * Champion - Brevet Admiral Glie'oleg Kru's flagship / Flagship of the fleet during the Battle of Kalarba
 * Megador - Grand Admiral Gilad Pellaeon's flagship / Flagship of the Galactic Alliance Defense Fleet
 * Right to Rule - Grand Admiral Gilad Pellaeon's flagship
 * Poesy - Commodore Mabettyte's flagship / Flagship of the New Republic/Duro fleet at the Battle of Duro
 * Ralroost - Admiral Traest Kre'fey's flagship / Flagship of the Galactic Alliance Defense Fleet
 * Elegos A'Kla - General Garm Bel Iblis' flagship
 * Bail Organa - General Garm Bel Iblis' flagship
 * Mon Adapyne - General Keyan Farlander's flagship
 * Mon Mothma - General Wedge Antilles' flagship

Ssi-ruuvi Imperium

 * Shriwirr - Flagship of the Ssi-ruuvi's invasion fleet

Duskhan League

 * Pride of Yevetha - Nil Spaar's flagship / Flagship of the Duskhan League

Yuuzhan Vong

 * Legacy of Torment - Shedao Shai's flagship during the Battle of Garqi as well as the Battle of Ithor
 * Kur-hashan - B'shith Vorrik's flagship
 * Sunulok - Warmaster Tsavong Lah's flagship / Flagship of the Yuuzhan Vong Fleet
 * Blood Sacrifice - Warmaster Tsavong Lah's flagship / Flagship of the Yuuzhan Vong Fleet
 * Yammka - Supreme Commander Nas Choka's flagship
 * Yammka's Mount - Warmaster Nas Choka's flagship / Flagship of the Yuuzhan Vong Fleet