Monsanto is in the news now. IG Faber has split into many independent companies and doesn't exist anymore.
(IG Farben manufactured the Zyklon B that was used in the gas chambers).
I'd guess the association of "IG Farben" with the gas chambers is very strong, but that brand ceased to exist in the 1950s. The name "Bayer" (from my perspective) never has been associated with it that strongly.
And I suppose IBM warrants a mention for doing business with Nazis.
The Fanta drink originated as a cola substitute in Germany under a World War II trade embargo for Coca-Cola ingredients in 1940. . . . In February 2015, a 75th-anniversary version of Fanta was released in Germany. Packaged in glass bottles evoking the original design and with an authentic original wartime flavor . . . An associated television ad referenced the history of the drink and said the Coca-Cola company wanted to bring back "the feeling of the Good Old Times".
I understand that in complex business sometimes controversies arise, but by they went straight evil during WWII (ie using Auschwitz prisoners killing many)