Quoted from Wikipedia:
Numerous aspects of the storyline differ in the PC version. Before reaching the Citadel, Drake must pass through the small village of Cador-Sûl, which is not present in the PlayStation version. Also, Prince Dain must be rescued from the Ironpicks before he can be spoken to, and Tor is not present. Two dungeon-like locations, the Catacombs and the fallen Starship, are accessible only in the PC version. Ursan plays a larger role, Celestia does not flee Citadel and the final battle takes place on Necros' Battleship, with no mention of the Kreegan Gate.
Numerous aspects of the storyline differ in the PC version. Before reaching the Citadel, Drake must pass through the small village of Cador-Sûl, which is not present in the PlayStation version. Also, Prince Dain must be rescued from the Ironpicks before he can be spoken to, and Tor is not present. Two dungeon-like locations, the Catacombs and the fallen Starship, are accessible only in the PC version. Ursan plays a larger role, Celestia does not flee Citadel and the final battle takes place on Necros' Battleship, with no mention of the Kreegan Gate.