Executor
Lord Vader's personal flagship, seen in The Empire Strikes Back and Return of the Jedi. The first ship constructed in its class. Built under heavy security at the Kuat Drive Yards shipyards at Fondor, shortly after the Battle of Yavin, as seen in Classic STAR WARS comics. Destroyed after impaling the second Death Star at Endor when the battle station exploded.
Reaper
Flagship of Scourge Squadron, an elite group of star destroyers which was formed for Grand Moff Tarkin and commanded by Grand Moff Ardus Kaine subsequent to Tarkin's death. Flagship of Kaine's Pentastar Alignment Imperial faction at a time approximately three years after the Emperor's death. Described in STAR WARS Adventure Journal #3.
Terror
Admiral Sarn's command ship appearing in the Rebel Assault II computer game, which is set sometime before Return of the Jedi. Some story elements in these games don't mesh well with the movies, so the status of the Terror in the overall continuity is uncertain.
Guardian
Flagship of Fleet Admiral Gaen Drommel. Was stationed in the Core regions near Coruscant at the time of Return of the Jedi. Immediately after word of Palpatine's death was received the Guardian departed to Drommel's home sector as part of his efforts to establish a small personal empire. Severely damaged in a battle with New Republic forces which took place not more than three years after Return of the Jedi. Survived until at least three years after Return of the Jedi [described in Wanted by Cracken]. Captured by New Republic agents more than a decade later [Two for One].
Vengeance
Commanded by Admiral Senn in Airam sector sometime between the battles of Hoth and Endor. Destroyed by a concerted and carefully-planned rebel attack [Balance of Power].
Aggressor
The flagship of Admiral Roek was stationed in the Inner Rim regions of the galaxy before the Battle of Endor. Six months later it was recalled to the Galactic Core to fortify and defend the shipyards of the Corellian system from potential rebel attack, as described in STAR WARS Adventure Journal #2. This ship, or another by the same name, remained in service and recognised the authority of Ysanne Isard two and a half years after the Battle of Endor.
Iron Fist
Constructed as Brawl (one of the earliest ships in the Executor-class) and presented to Admiral Zsinj by the Emperor. Renamed after his first command, a Victory-class destroyer. Infamous flagship of the renegade Imperial Warlord Zsinj and used extensively by his forces in campaigns concurrent with the New Republic's capture of Coruscant three years after the Battle of Endor, as described in the X-Wing novels. The target of a five month search by a New Republic naval task force led by General Han Solo, as described in The Courtship of Princess Leia, four years after the Battle of Endor.
Lusankya
Secretly buried on the surface of Coruscant during the reign of Emperor Palpatine, the Lusankya was used as a top-secret holding facility for prisoners of Imperial Intelligence. Three years after the Battle of Endor, this warship fell under the command of Ysanne Isard. This ship was equipped with an unorthodox repulsorlift bed enabling it to lift off the surface of the planet. Captured by Thyferran and independent forces aligned with the New Republic. Its exact ownership after that point is unclear, but (under command of General Wedge Antilles) Lusankya was decisive in capturing the Imperial planet Phaeda a few months following the demise of the last Palpatine-clone. Its absence from other major conflicts, such as the Thrawn and Shadow Hand campaigns, suggests that the repairs were time-consuming.
[unknown]
Another Super Star Destroyer remained in the sectors of the Galactic Core and recognised the authority of Ysanne Isard, Director of Imperial Intelligence who ruled from Coruscant two and a half years after the Emperor's death at Endor, as described in the X-Wing Rogue Squadron and X-Wing: Wedge's Gamble. It is possible that this ship is the Aggressor.
Knight Hammer
Constructed by warlord Superior General Delvardus and commanded by Admiral Daala approximately eight years after the Emperor's death. Plated with special "stealth armour" as a sensor countermeasure, which has the interesting side-effect of making the hull almost completely black. Described in Darksaber.
Intimidator
There are three of this class of starship in the Black Sword Fleet in Before the Storm, thirteen years after the Battle of Endor. One of them was originally named the Intimidator, according to Shield of Lies. This ship is supposed to exhibit design modifications which are distinctive of "late-production" SSDs, particularly an "additional shield tower located on the centreline". Intimidator became the Yevethan flagship, renamed Pride of Yevetha.
[unknown]
At the Battle of Orinda the New Republic fleet carrier Endurance was destroyed with its entire fighter compliment aboard in a concentrated Super Star Destroyer attack. This incident was recalled as history at the start of Before the Storm, but must have happened sufficiently late in New Republic history for the new government to have acquired or designed its own dedicated carrier vessels.