ZipSigner

This app signs update.zip files, APK, or JAR files using your own private keys or one of the four built-in certificates (media, platform, shared, testkey).

All output is automatically zip-aligned. ZipSigner can work with existing keystores, or you can create keystores, keys, and self-signed certificates with this app. JKS and BKS keystores are supported. A certificate's MD5 and SHA1 fingerprints, as well as the SHA1 key hash, can be copied from the key properties screen.

Think of this app as a combination of jarsigner, signapk, keytool, and zipalign.

The built-in keys and auto-selection modes will appeal to themers and modders. The ability to sign with private keys will appeal to developers. 

This app does not require root privileges.