We have two eyes, but we don't have two hearts. Why do humans have two of some organs, but not all?
Here is my overly succinct answer.
I doubt we will ever know this for sure. But, it basically comes down to ancestral bilateral symmetry in development; this defaults to two organs and is broadly symmetrical except where the organs are central. See this article for a more thorough answer regarding bilateral symmetry.
Further exceptions to symmetry occur where evolution pressured the body into not bothering to grow the second of an organ due to a waste of resources for the body, or functional advantages emerged from asymmetrical evolution. I always like the ears of an owl for an excellent example of two asymmetrical features that provided a discrete advantage when it comes to locating the source of a sound.
For some organs, the function is really dependent on having two: two eyes offer the possibility to appreciate distances, two ears to appreciate directionality of sound and to balance oneself.
Bilateral symmetry is both a good way to obtain these twinned organs, and may also be physically easier to obtain in the course of evolution (see the work by Vincent Fleury, University Paris Diderot, e.g. http://www.ncbi.nlm.nih.gov/pubmed/21784360). Perhaps this is mechanically quite advantageous to have symmetry for balance reasons. You'll note that the vehicles designed by the human are mostly symmetrical too.
This may explain why there are two lungs, e.g. Two brain hemispheres are justified with a symmetric body plan as many anatomical features are mapped directly in the brain geometry (see Fig 5.6 in http://www.bem.fi/book/05/05.htm, of course sensory and motor are in both hemisphere). But evolution has also been able to depart from this symmetrical plan when having twin organs would be more of a coordination nightmare: e.g., two hearts would make it difficult to have a sensible circulatory system (at least some dyssymetrisation would be needed so that they would direct the flow in the same direction! [no reference on that, you can draw a symmetric circuit with two pumps and see for yourself])
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