well the difference is that a content-based regulation is, as the name suggests, one that regulates based on content -- like regulating porn.
Content neutral regulations are regulations like licensing regulations - not based on content. Content based regulations are subject to greater scrutiny. "[i]f a statute regulates speech based on its content, it must be narrowly tailored to promote a compelling Government interest. If a less restrictive alternative would serve the Government's purpose, the legislature must use that alternative."