I agree with what Reflog said, my company used an ant script to change the package name for each brand, and also to replace resources as needed. I wrote the base app with default behavior in mind, and created folders for each additional brand containing only those files that were different from the base, just like the multiple drawable folders with different dpi sizes ("drawable", "drawable-hdpi"...). Other changes included modifying the strings files for each brand for appropriate colors and legal text.
By naming them in the localization style (for instance "drawable-en-rAA-hdpi", "layout-en-rBB"...), I was able to test this quickly in multiple emulators by opening the "Custom Locale" app in each emulator, and setting the locale to "en_AA", "en_BB" as needed. By saving multiple copies of the base AVD, I was able to save those settings so I didn't have to switch within the emulator to test all the final brands.
One caveat to this approach is this emulated version of the app will include all the files in the .apk, while the ant script strips out the duplicates. Also, while this "full" .apk will install on devices, it will only show the default behavior unless you can set the locale on the device to match the brand locale. (Custom Locale was not installed on any of my physical devices.) This works well if you intentionally use existing named locales (en_AU, en_CA, en_GB), but can be problematic for custom names (en_B1, en_XX).