In the beginning, there was darkness (or is that Darkwing?). The nefaroius arch-crimanal, Turbus Bulba was in jail and making licence plates, or so it seemed. In reality, he was making evil deals inside his jail cell. He sent his stooges Hammerhead and Hoof and Mouth to capture the Waddlemeyer Ramrod as well as the creator's Granddaughter. They only managed to get one of those things: the Ramrod.
The Fearsome Five (Bushroot, Megavolt, Quackerjack, Liquidator, and Negaduck) once took over St. Canard Tower along with the rest of the city and used it as its headquarters. They were trouted by the Justice Ducks.
Dark Warrior Duck
When Gosalyn went to the future, she found out that her dad, Darkwing Duck, had become a crazed (more than usual) vigilante who controlled St. Canard and its citizens with a literal iron fist. Any one who broke any of his strict laws would be sent to prison, without any hope of release even for little crimes like not being in bed by 8:30 or ripping the tags off matrices. Dark Warrior Duck (as Darkwing was then known as in this now alternate reality) used St. Canard Tower as his base.
Quackwerks (or Bulba takes his bow)
When the evil coperation known as Quackwerks took over St. Canard in only a year (in the Duck Knight returns), it used the tower as its headquarters. This building was were everyone worked, both the former criminals and the St. Canard Police worked there (including our hero: Darkwing Duck). When It was revealed that the man (or bull) in charge of Quackwerks was non other than Taurus Bulba, and the former criminal/turned robot/turned Corporate CEO was defeated, Uncle Scrooge gave leadership of Quackwerks to Launchpad McQuack.
This is a symbolic gesture that Bulba chose the St. Canard Tower to be his new Headquarters, because it was the sight of his first meeting with Darkwing Duck. It can be said the fact he chose to live above the tower shows he believes he is above such things as his former life promoted. Although he most likely will return later on, it is significant that the site of his first adventure with Darkwing duck would be his last.
With Launchpad operating as the new CEO, Darkwing using the tower (or at least a floor of it) as his new hideout (in the place of the Audobon Bay Bridge) to hold the Thunderquack and to train Gosalyn to be a super hero as Gosmo Duck (formally). However, he quickly returned using to the Audubon Bay Bridge.