Android applications are shipped as "packages", which are compressed archives with class files, resources, and meta-information (the AndroidManifest.xml file and security certificates) for the application.
A package has the extension .apk, and it consists of a set of directories and files in a gzip'ed archive.
A package usually contains the following items:
META-INF/MANIFEST.MF The manifest file for the package file (apk) itself.
META-INF/CERT.SF A security certificate
META-INF/CERT.RSA another security certificate (should distinguish these two)
AndroidManifest.xml The manifest file for the application(s) in this package
classes.dex The actual code for the dalvik (http://eLinux.org/java) classes for the application(s) in this package
res/ a directory containing resource files
The AndroidManifest.xml file has information about the application(s) in a package. Usually, a package will contain a single application. The AndroidManifest file describes the application's name, as well as libraries and security permissions neede by the app, messages used by the app, what icon to use to represent the app, and more.
Tools for managing packages
The aapt tool is used to create, inspect and modify Android packages.
An overview of application resources is at: http://developer.android.com/guide/topics/resources/index.html
It is possible to use a raw file as a resource (without it getting compiled by the build system). See this article on using raw files as resources in Android.
Assets are like resources, except that do not have a resource ID, and they are listed in the 'assets' directory of a package, rather than the 'res' directory.