The mechanism that determines whether you have fish fins or walking limbs is the rate at which a couple of hox genes are expressed. Hox genes are like conductors of an orchestra - they regulate how a whole suite of other genes perform, and changing the rate of a hox gene's expression can radically alter how an organism develops.
So if you're a fruit fly, how your hox genes are expressed will determine how your legs, antennae, and wings develop, but if you're a human, your hox genes will determine how different parts of your vertebrae develop.
To get a better insight into how hox genes work, earlier this year developmental embryologists inserted the hox genes from a fish into a mouse. The fish hox gene couldn't produce fingers and toes in the mouse, says RiAus's A Week in Science, which means the genetic apparatus to develop these digits must have evolved after walking limbs developed.
We also now know how breathing developed for the first time in our earliest ancestors - and as weird as it sounds, we almost ended up breathing out of our ears. Found out how by watching A Week in Science above.