With a highly elliptical gas giant in the neighborhood, the smaller planet in these simulations would cycle between habitable and uninhabitable conditions, sometimes with a period of just 1000 years. It could support life as we know it sometimes, but other times be frozen over, or boil off all of its water.
This has serious implications for the search for Earth-like planets, which is expected to ramp up as Kepler continues its three year mission. Just because a planet is in a good spot now, it might not always be, depending on its environment. As biological evolution on Earth has shown, a lot of time is needed to build up complex organisms.
If this is too depressing for those of you hoping to find life elsewhere, I have the solution. Push around your own little Earths! PhET Interactive Simulations at the University of Colorado has a really fun gravitational simulator called My Solar System. With just a little bit of fiddling, I was able to get a large planet in an elliptical orbit and a smaller, closer planet with a range of orbits. Warning: you will get really distracted making your own wacky solar system, so don't plan on doing any work for a while!