I don't know how/if it's possible to mix both, for example embed a NME app inside an Appcelerator app (besides using UI.WebView and embed it as HTML...)
You can compile this example to both Flash and JS online.
If you install Haxe and NME (http://haxenme.org), you can also compile it to iOS, Android, WebOS, BlackBerry, as well as desktop Mac, Windows and Linux binaries.
And these are only the possibilites offered by NME, which is basically a Haxe-based Flash API implementation.
Most standard classes and methods (String, Array, Hash, etc), and a lot of third party libraries are completely cross-platform, so you don't need conditional compilation.
Usually you use conditional compilation either for very low-level per-platform operations / optimizations, or to switch, say, between client code and server code, like here for instance: