Goa'uld Flagship
A few of the more prominant Goa'uld have at their disposal a massive and heavily armed Flagship alongside their fleets of Ha'tak-class Motherships.
Apophis's Flagship
Apophis' Flagship was a spacecraft that Apophis obviously used as his flagship after he had taken over Sokar's forces and territory. In 2000, Apophis took his flagship to the homeworld of the extinct Tobin to negotiate an alliance between him and Heru'ur[1]. He continued to use this ship as his flagship until its destruction in 2001, when he had the ship self-destruct to prevent it from falling to the replicators[2].
Apophis' flagship has numerous advantages over normal Ha'tak including faster hyperdrive, better shields, and weapons capable of destroying a Ha'tak in less than a dozen shots. It is several thousand meters long.
Anubis's Flagships
Anubis' Flagship was a spacecreaft several kilometers long with a wide array of technology based off of Ancient technology. It's main weapon is capable of destroying a few Ha'tak motherships in a single shot. It is also capable of causing massive destruction on a planet. In 2003, it was destroyed over Langara[3]. By early 2005, Anubis had constructed another flagship without the main weapon of the original. This second flagship was later destroyed in orbit of Earth by the Ancient superweapon in Antarctica[4].