What technologies are in demand? I see J2EE (whatever that means to some people, that's a lot of technologies in there), Hibernate, JUnit, HTML/CSS/JQuery.Given that Java is one of your stronger areas, and given how much demand there is for Java developers, I'd suggest you continue to focus on Java and related technologies. In that area, you'd probably be well served to learn Spring (the core DI framework), Spring MVC, and Spring Data / JPA... make sure you have a decent knowledge of SQL (you don't need to be a DBA, but some low level SQL never hurts). Knowing the "raw" Hibernate API won't hurt, but JPA is really where it's at these days.
String knowledge of the core Java language is always good as well. Java is a pretty big language/library, but get to know the Collections APIs, the IO APIs, at least a basic understanding of threads / threading (including the java.util.concurrent package), and maybe some basic knowledge around using sockets in Java.
If you have (or can claim) that knowledge, you're in decent shape for a lot of Java oriented positions. Beyond that, knowing the low-level servlet API is still valuable, as well as some of the more popular 3rd party libraries... get to know Quartz, Lucene, Apache Camel, etc.
Learning basic administration skills around at least one Java application server (JBoss, GlassFish, Geronimo, whatever) is always good.
Learn as much as you can about Tomcat.
Knowing how to build web-services (both old style SOAP and RESTful services) is good. Look at JAX-RS and Apache Axis.
Get a handle on all of the previously mentioned tech, and you'd be pretty in demand in the Java world (unless you live somewhere really desolate, where there just isn't any demand for tech jobs!).
If you want to move onto some of the new'ish stuff that's catching on and becoming "in demand" I'd say spend some time learning Hadoop / HBase, Storm, S4, Kafka and maybe another NoSQL database like MongoDB.
Would a J2EE certification help? It might not make a difference to the startup guys here on HN, but would Java experience, no J2EE experience but J2EE certifications get me in the door somewhere?
This is always a controversial question, but my take is that "yes, certifications do help." The question is "how much do they help?" and "where do they help?" At a startup, maybe not so much... at your typical Fortune 500 $BIGCORP, they probably do help. A certification alone isn't going to get you a job if you have NO skill, but if you're competing with somebody else for 1 position, and you both have roughly the same background, and you have certification and the other guy doesn't, it might just tip the scales in your favor. BUT... if you pursue any certifications, do it right... USE the experience as an excuse to do a "deep dive" into whatever, and actually LEARN. Don't just download "brain dumps" and cram for the test. Studying for a certification test can be very useful, I learned a lot studying to get my SCJP back in the day. Doing the certification was it's own reward, even if the actual cert never helped me land a job.