Experiment with different angles in your photos. Ever notice how old films by Alfred Hitchcock, for instance, contain so much drama when sometimes very little is actually going on? Part of the reason for this is the camera angles used. Depending on the perspective of the viewer, the subject can look terrifying in nuanced ways, all because of the camera angle.
Photograph your subjects at a low-angle, gazing upward. This can be frightening for numerous reasons, particularly because it has brought a spooky perspective to the subject. Lots of old film noir, horror, and crime capers use this type of low-angle technique. Try it out on your subjects and see how just lowering the height of the camera to the subject can add a layer of subtle creepiness.
A high angle also can be an unsettling way to picture your subjects. This works when you have a higher elevation than your subjects, maybe from a window or a ladder. By looking downward at your subject, the camera is slyly suggesting that the subject is powerless, overwhelmed, or totally swallowed up by its surroundings.
Another ominous angle worth playing with is the "Dutch tilt." This is done by simply angling the camera off to one side, at an oblique angle. This is a trick often used in cinema to suggest tension or uneasiness in the scene. Similar results of uneasiness can be achieved by anti-framing or other framing techniques that might not be normally used. Try making the focus of the photo unclear, such as placing the focus off to the side or low in the composition. Not only does this work well with people as the subject, but also with buildings or nature scenes.
A lot of mood and feeling can be suggested in your photos by using contrasts in light and dark imagery. Shadows hold mystery, and using black-and-white film also can add an air of mystery and intrigue that color cannot.
Try shooting in black and white. There certainly is a romance and a certain challenge to black-and-white photography. Combined with different angles and lenses, you might get some startling results that add just the sinister element for which you are looking.
Use a lot of darkness in your photos. From early on, people have had irrational fears of the dark; what child does not use a night light or have instances of being afraid of the dark? Use darkness in your photos to explore psychological aspects of your subjects. Use basic lighting or whatever natural or man-made light that is available. For instance, if you are shooting a subject outside and the trees are casting long shadows, instruct your subject(s) to stand in the shadows. Photograph them there, and see how the effects can add an eeriness that was not there before.
Use lens flares in your pictures to add an aspect of alarm, drama, and/or confusion to the composition. This is best achieved by allowing a bright light source (like the sun or a street lamp) to reflect off your lens. The resulting image might then look hazy, washed-out, or have "sun dogs" that will add sudden urgency if used correctly. The only way to really do this well is to practice and see what works best. Depending on the situation, this technique might be very effective or not work at all.
When taking photos, it's best to consider your role as photographer to be similar to that of a painter mastering the canvas or a director making a film. You can give your subjects direction and pull out performances from them, or, if you are filming objects, manipulate them in ways to draw out depth and emotion from the viewer.
Have your subjects role-play. Maybe you have given them some props or some wardrobe or a little makeup. This can be effective, but so can simply asking them to turn away and make their lower lip tremble. Talk to them about something that makes them nervous and photograph them reacting to your instructions.
In situations in which you have control over the setting and subjects, work this to your advantage. Dress the set to appear creepy, play around with the space and make it look uneasy and odd. Have fun projecting a little fright into the environment for your pictures and you might just surprise yourself.
Take lots of photos. It might take a while before your models are relaxed enough to really perform and react well. And why take one good photo when you can take several? Take a lot. It might just be that after a dozen or so photos you have hit your stride -- your subjects are really reacting, the light is right, and your ideas are really starting to show. Have lots of photos to choose from in the end and you'll be all the more pleased.