It can be a bit difficult to differentiate between truly famous and just notable zoo animals, but off the top of my head...
- Incas (prior to 1885 – February 21, 1918) the Carolina parakeet, famous for being an endling.
- Oliver (c. 1957 – June 2, 2012) the chimpanzee. Also known as the "Humanzee", Oliver was purported to be a missing link or hybrid, based on his unusual appearance and behaviour. In reality, he was genetically an ordinary Pan troglodytes, who'd been exploited and mistreated most of his life.
- Northern white rhinos Sudan (c. 1973 – March 19, 2018), Najin (c. 1989) and Fatu (June 20, 2000), all famous for being the last living representatives of their subspecies. Honourable mention goes to Nola (August 21, 1974 – November 22, 2015), the last northern white rhino exhibited outside of Africa.
- Keiko (September 24, 1976 – December 13, 2003) the orca, known for starring in the film Free Willy (1993) and for the subsequent attempt to return him to the wild from captivity.
- Tilikum (c. December 1981 – January 6, 2017) the orca. Perhaps the most famous animal on my list, lauded within both pro-caps and anti-caps communities, and perhaps most well-known for killing trainer SeaWorld Dawn Brancheau in 2010.
- Emi (c. 1988 – September 6, 2009) the Sumatran rhino, matriarch of the current captive population of her species.
As for famous/notable individuals I've seen in person, I'd say
Aurora, the last of the Vancouver Aquarium's belugas, who died just nine days after her 21yo calf,
Qila, passed away, counts as one. Both whales' deaths were ruled the result of an unknown toxin, and I remember there being a lot of media attention on the situation. As well,
Boomer the lion, the only of the Greater Vancouver Zoo's animals
to have spent a night in jail. His backstory and the subsequent legal ordeal was covered in the news, and he's now arguably the zoo's most popular animal (if you don't count the red pandas

).