I agree with Kosi2801. Class file encryption is just imitation of security (see http://www.excelsior-usa.com/articles/java-obfuscators.html)
Use of custom ClassLoader's can break the application, e.g. in Application Servers.
There is the better way: use encryption of String constants in a class files. The most of commercial obfuscators have this function, for example Allatori, Stringer Java Obfuscation Toolkit, Zelix KlassMaster, Smokescreen, DashO (super expensive). The Stringer Java Obfuscator has call context check and integrity control features which makes protection really hard to hack.
The most secure way is to store and execute parts of bytecode on an external device like JavaCard.
N.B. I'm CEO at Licel LLC. Developer of Stringer Java Obfuscator.
