i was just today looking at the penguin 350 and emperor 400 at petco. First, i think i would shop around, because the prices vary GREATLY on these filters from shop to shop to online retailer. find an LFS that makes you happy or grab em online :)
as for the two themselves the only real difference i could tell was overall build quality. the emperor just seems a little more... "sturdy" i guess you could say, but when i say a little more i mean a LITTLE more. i didnt see anything with the emperor that would get me to spend the few extra bucks over the penguin, and ive talked to alot of people that swear by the penguins. I, myself, will be getting a penguin for my next filter. I might even get two penguin 350s for my 110 gallon tank.