On the TV-series Charmed in the episode The Power of Two, Phoebe and Prue hunt the ghost of a murderer executed at and until now haunting Alcatraz who has now escaped to the mainland and started killing again.
Midtown Madness 2 has San Fransisco as a playable level, where Alcatraz Island is viewable in the distance, though it is not reachable.
In the DC Universe, there is a metahuman prison located on Alcatraz Island. The new Titans Tower is built across from it, both as an intimidation tool and as a way to provide instant metahuman support in the case of a breakout.
The prison is also featured in the game, C&C Red Alert 2 Yuri's Revenge , which Yuri used the island for his psychic dominator superweapon.
At the Winston Cup(now Nextel cup) race at Infineon Raceway in 2002, it was toured by Jeff Gordon and Chris Myers in the pre-race show.
The Andy Griffith Show episode "The Big House", Barney Fife(Don Knotts) makes a reference to "the Rock" when he tries to make the Mayberry courthouse a big city jail.