One of the best ways to make sure your home is not simply unique but also remarkable, is to renovate an unusual building. Some options for renovation include old school houses, former factories or mills and, of course, churches.
The most important thing to ascertain is the soundness of the structure, since even a small church is a relatively large building and it would cost vast amounts if you were to find it needed underpinning or to have supporting walls replaced. A thorough survey will make sure that this doesn't come up. If the church is a listed building, you need to be well-versed in what is expected of you and what you are allowed to do. Your local planning authority can give you all the information you need.
If the property is considered to be of special interest because of its age or historical significance, you may be able to get advice or grants from such bodies as English Heritage or The National Trust, depending on the location of the building. Once you know you have a solid structure, you can turn your attention to the interior. You can restore with consideration to the age and style of the building, and make use of fittings, such as the choir stalls, sanctuary or confessional boxes, but there is no reason why the interior shouldn't be entirely modern in appearance.
When you buy your church, you may be lucky enough to have original windows in place, in which case, you should use their positions to plan any major internal alterations; you wouldn't want a staircase to obscure a beautiful piece of stained glass, for example. If the church has pews, you may find that you can reclaim the wood from any that you don't need for door frames, doors, panelling or cupboards to keep an authentically aged feel.
The beauty of using something as unusual as a church for a dwelling is that you are unrestricted by convention. There are no expectations about what a church/house should be, so the only important thing is that you are happy with it.