serialization - Howto base64 encode an java object using org.apache.commons.codec.binary.base64? - Stack Overflow

Actually the commons-codec version and specific Sun internal version you are using do give the same results. I think you thought they were giving different versions because you are implicitly calling toString() on an array when you do:

System.out.println(org.apache.commons.codec.binary.Base64.encodeBase64(baos.toByteArray()))

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