Heights are no good. Can't climb a ladder. Can't stand on chairs. Need a railing to go up stairs, and I'll stay as far away from the well as possible. I tried to ride a horse when I was 4, and years later my parents said they thought I was afraid of horses. No, it's because they're so high off the fucking ground. Bicycles are no good either. The feeling of losing my balance and falling makes me wanna die.
Darkness. But not actually? I kind of enjoy the dark. But when I look around in the dark, I see things that aren't there. My imagination plays tricks on me, turning a harmless chair into a skulking monster, or plastic bag into a creepy face. This is also the reason why I can't handle oceans or deep water. The water itself isn't a problem, it's the fact that things can come at me from any direction and I won't see them.
And People, I guess. Normally it's fine, but I always have the knowledge in the back of my head that things could go wrong. A drunk driver could plow through my house; a random person on the street might go berserk and start attacking people; a long time friend might suddenly cut ties without saying why; a relative may have an unexpected illness.
To integrate them into a story...? The second two basically amount to 'surprise'. Just explain to the reader how things are or how they're supposed to be, and then subvert those expectations. The peaceful night is suddenly filled with a stalking monster, within easy reach of you.
For the heights? I think that one's too personal. You can't really describe something that's a real phobia. Even if I say you're standing a thousand feet in the air, on wobbly piece of rope, swaying in the breeze... You won't feel it. You're just reading, not actually experiencing it. And even if you were, you might not fear it. You might get a thrill, or just not care more than 'Oh, I probably shouldn't fall here.'
