I asked this in a thread on Slashdot once, and got a really good answer. Basically, there are a number of molecules that can have a left or right chirality. These happened by random chance at the beginning instances of abiogenesis, and were replicated faithfully since. So if it happened twice, a number of those molecules (or larger structures) would be backwards. From a macro perspective, things like the heart being on the left side, or the direction of other internal organs (i.e. appendix on the right side). At the molecular level, things like the spiral of DNA. There is some more information in Wikipedia, under abiogenesis and homochirality.