I would say many nowadays are 'man made'. Popular species like guppies and goldfish have been selectively bred for form and colour that some of them no longer even resemble the wild stock they originally descended from. However, here is a list of other fish that have been quite majorly altered.
Glofish (modified zebra danios)
Blood parrot fish
Any of the popular cichlid hybrid crosses
I am not really familiar with popular crosses as I do not keep or have an interest in cichilds. However, I have seen a few hybrids such as red-tail catfish (not a cichlid) crossed with a tiger shovelnose catfish and ones using jack dempsey cichlids on the Monsterfishkeeping forum.
I think that the Blood parrot is one of the worst of them. Talk about an ugly looking fish.