There are too many examples to name but the big ones are the Dutch East India Company, Nationalized Railroads in the US in WWI and more recently the "Bailout" of banks in the wake of the real estate collapse.
What we've yet to see in history is a corporation that directly and openly challenges a state for sovereignty. I've written in the past that it would be technically possible for a large corporation to raise an army/navy,buy land and declare sovereignty, but that none deign to do it.