Its complicated :)
In short - Hox genes, a whole bunch of related genes which govern the general layout of the body of the animal/human.
http://en.wikipedia.org/wiki/Hox_gene
After that, it comes down to a whole load of inter-related regulatory networks, most of which are still poorly understood. Mitochondrial regulation, for instance. Epigenetics. And then you have relational control; Cells are instructed to stop growing when they meet cells of a different type, signalled by chemical messages. And finally, there is a growth limiter built in, again through genetics, and once a cell has achieved its growth target - it stops.
So how organs are formed and created, how they know when to stop growing, how these organs are laid out within the body are all governed by a complex inter-relationship between all of the above systems, and some I have not mentioned for simplicity.
You might also be interested in this discussion, taken from "The Naked Scientist" forums, on exactly your issue.
Scan down until you see the contribution from "Nizzle" (14/09/2009 05:25 ish) who offers a more detailed overview of this process.
http://www.thenakedscientists.com/forum/index.php?topic=25283.0