I have a fair bit of experience with both. Good friend has an '09 3s hatch, several have assorted 4-door Civics both regular and Si.

Interior build quality on the Civic is a bit nicer (although the layout's weird) and it gets better mileage.

3 can have more luxo features, more character to drive, hatch is more useful for carrying crap.

Do you really need built-in navi when a portable GPS or a smartphone will do the trick?