C. elegans (a type of nematode) is even simpler, with exactly 302 neurons and ~15k synapses. But despite having the complete connectome, there has to date been only limited success at simulating the whole worm. Although see: https://code.google.com/p/openworm/
Worms (C. elegans specifically) have specific well-documented responses to certain stimuli. You can apply those same stimuli to your simulated worm and see if it responds like a typical real worm.
Actually that's pretty much what they are. There us a whole battery of stimulus stimulus-response tests that are essentially used as a regression test suite to figure out what deleterious (or even beneficial) effect a given mutation has. Of course these "tests" must be manually carried out by researchers on live worms.
Edit: Also see the NYT article below.