<p>Within an application, I've got Secret Keys uses to calculate a hash for an API call.  In a .NET application it's fairly easy to use a program like Reflector to pull out information from the assembly to include these keys.</p>

<p>Is obfuscating the assembly a good way of securing these keys?</p>

Probably not.
Look into cryptography and Windows' built-in information-hiding mechanisms (DPAPI and storing the keys in an ACL-restricted registry key, for example). That's as good as you're going to get for security you need to keep on the same system as your application.
If you are looking for a way to stop someone physically sitting at the machine from getting your information, forget it. If someone is determined, and has unrestricted access to a computer that is not under your control, there is no way to be 100% certain that the data is protected under all circumstances. Someone who is determined will get at it if they want to.