Constitution class Enterprise, commanded by Kirk, would be the winner. Kirk always found a way to cheat death, and to turn it into a fighting chance to live.
I was thinking about making the poll "Toughest species". So far I got: Tin Man The Prophets/Wormhole Aliens The Pah-wraiths Species 8472 The Borg The Hirogen The Douwd The Kelvan Any more?
The Hirogen beat one wounded 8472, that doesn't mean the Hirogen can kill 8472s. Part of it depends on the level of prep. If nobody has time to develop the 8472 antigen, 8472 win easily.
The Hirogen ship could hide in a star (and their armor can withstand the heat of a dying star), that has got to make them worthy foes.
I'll add Remans, and I don't know why I forgot about the Caretakers... and Humans. I'll post the thread tomorrow.