I assume we're talking about Christian fiction here, and unfortunatly that's a very short list.

I don't know whether you'd count them as Christian fiction, but they are at least fiction with Christians in: The Sparrow and A Canticle For Leibowitz. That latter comes with a slightly cynical attitude towards the Church, although not towards Christianity itself, but it's one of the best sci-fi books of any religious persuasion I've ever read. (And even that could be called disparaging it: if, as I'm rather ashamed to admit I sometimes do, you draw a line between "sci-fi" and "proper novels", they're definitely on the "proper novel" side.)

The Sparrow has a sequel, which I haven't read. Edit: Oooh, so does A Canticle For Leibowitz. I might have to look for that.

Peter