Is there a way to load a different cacerts than the one specified in the java_home/jre/lib/security folder?

I think you want to specify the truststore:

java -Djavax.net.ssl.trustStore=/home/gene/mycacerts ...

Or if you are using certs through JSSE (you probably are), you can copy your truststore to jssecacerts in the $JAVA_HOME/jre/lib/security/ directory (although you’d still have to do that each time a JDK got installed/reinstalled). Sun’s JSSE looks for $JAVA_HOME/jre/lib/security/jssecacerts before $JAVA_HOME/jre/lib/security/cacerts.

See http://java.sun.com/javase/6/docs/technotes/guides/security/jsse/JSSERefGuide.html#X509TrustManager