Basically I want to be able to encrypt and decrypt with AES 256. What is the industry standard library for encryption in Java? Something that has been around a long time and is tried and true.
How bout the Java Cryptography Extension. JCE used to be an optional extension, now it's been integrated into Java 2 SDK
http://java.sun.com/j2se/1.4.2/docs/guide/security/jce/JCERefGuide.html
In what context? The JRE contains the primitives for encryption, and support for TLS/SSL. But there's not much out of the box for encrypting stand-alone blobs of data, or even files.
The Bouncy Castle API's have been around a while, and have API's for using OpenPGP or S/MIME and CMS for file and email encryption.
By the by - if you want to use 256 bit keys, you'll have to install the "Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files". You can find them at the bottom of the Java SE Downloads page.
The export of strong cryptography is regulated, and you have to claim to not be in the Axis of Evil before you can unlock it.