Excuse my cross platform ignorance but, although I am currently only targeting my game @ Windows, I would like to maintain my code as cross platform as possible. Can I freely use conditional compilation directives such as:

#define identifier

#ifdef identifier
// code
#else
// code
#endif

and expect those to be implemented by the target compilers on the other platforms?

You can, but if you are using the EE 2.0 code editor, it doesn't recognize them across multiple files.
I'm counting on being able to use the engine versions like EE_MOBILE.

Thanks for the quick response Rubeus.

EE already has some predefined macros which you can view in the Esenthel headers, such as:
WINDOWS
MAC
ANDROID
IOS
X64
MOBILE

To my knowledge this is the recommended way.

My interest was more in providing conditional compilation to exclude embedded tools code when doing a game release as opposed to conditional compilation to do with platform targets.

I just put all my configuration and tools/debug info into 2 files. Not the best solution, but it works.

There is also following macro available:
DEBUG (when in debug mode)

and

const bool EE_RELEASE; (which is always true for publishing)