After many hours trying to build cert files to get my Java 6 installation working with the new twitter cert's, I finally stumbled onto an incredibly simple solution buried in a comment in one of the message boards. Just copy the cacerts file from a Java 7 installation and overwrite the one in your Java 6 installation. Probably best to make a backup of the cacerts file first, but then you just copy the new one in and BOOM! it just works.
Note that I actually copied a Windows cacerts file onto a Linux installation and it worked just fine.
The file is located in jre/lib/security/cacerts
in both the old and new Java jdk installations.
Hope this saves someone else hours of aggravation.