Meh, not a big bifference really. If you subscribe to the "don't throw out filter cart's" then stick with the Penguin because of the bio wheel. That said though... Nitrifying bacteria grow EVERYWHERE they can get oxygenated water, so really it doesn't matter.
Personally I'm not a fan of the Bio wheel (or any filter that specificly encourages growth of bacteria in one spot) only because it's kinda like putting all your eggs in one basket.
The biggest criteria for a filter IMO is how efficiently it removes particulate matter. That means it needs VERY little bypass, that's where the penguin is strongest IMO. Aqua Clears and Fluvals have bypass built right into them. Still use AC's though... What can I say? Their cheap lol!
At the risk of getting flamed here... I bleach my filter sponges about 2 or 3 times a year... Oxidizes out any organics that may not get rinsed out at cleaning time. If a tank is maintained properly the bacteria in the substrate, glass, decorations ect. will pick up any slack. Gotta remember the bacteria eat the fish waste, so there are only as many bacteria in the tank as there is "food" for them. The combined surface area of EVERYTHING else in the tank is in most cases larger than the surface area of your sponge/cart. The only time I'm ever worried about bacteria in a filter is during cycleing and with an overstocked tank. At those times you NEED all the bacteria you can get and it's harder (for a lot of reasons) for the bacteria to "catch up" after a cleaning/change.
Chris