I'm mostly talking about street self-defense, and your ears and eyes, I figure if they went for your mouth you clamp down. Edit: I should have been more clear, sorry, I meant from within the clinch.
Adding onto mattm's answer, there is no single way to defend against a basic attack. Street self defence is serious, which means there is no referee/coach there to tell you which techniques are allowed and which aren't. Everything you do will be heavily dependent on the situation and personal ability.
- How close is your attacker?
- How strong is your attacker? Will you be able to block the attack?
- How much movement space do you have? Are you cornered or free to run away?
- Does your attacker have a weapon?
- Do you have anything that can be used as a weapon?
With that being said, fish hooking is a close range technique that requires both arms. Since both your attacker's arms would be occupied, there's a pretty good chance you'd be able to land the classic kick-in-the-groin-and-run. (Is that taboo here? I haven't been around for very long)
You don't need to specifically defend against it. If someone is committing their hands to poking your eyes/mouth/ears/nose or whatever, you have free reign to choke them unconscious. To do this from the clinch (like you suggested) you would take them down, or go for a standing arm triangle choke, guillotine, or standing back take to rear naked choke. Now that they're unconscious, run away, beat them to death, do whatever you want. Fish hooks and eye gouges are easily the most overrated technique by untrained folk, right next to groin shots.
There's a funny Bas Rutten (Pride, Pancrase, and UFC champion, MMA legend) story about how he deals with eye gouges: