From the standpoint of resume building, I think a tool based cert looks really good, like a certification on IBM's Rational Application Developer tool, or something similar. I feel the same way about databases - like a DB2 cert or something. Nobody ever knows enough about databases.
If you really want to understand your environment, getting an application server certification would be good. That'd really help you understand the deployment and runtime environment, which means you sort of have to know everything.
To offer an opposing view point, I think it all depends on what portions of Java EE your company works in, which ones you're interested in, etc, as to which ones I'd recommend pursuing.
I do agree with Cameron that if your company uses one specific application server for their products, and that application server has a certification specific to it, that one might certainly be a good fit for your career. It would also have the bonus of being something your company could advertise (as mine does with regards to those of us who have specific certifications that apply to our products).
On the other hand, there's also something to be said for the standards-specific certifications, if you're looking in a more generalized direction. There's SCWCD (JSPs and Servlets), SCBCD (EJBs) and SCJWSD (web services) to choose from to start with, any of which would be a good launching point for adding to a resume.
Theodore Jonathan Casser
SCJP/SCSNI/SCBCD/SCWCD/SCDJWS/SCMAD/SCEA/MCTS/MCPD... and so many more letters than you can shake a stick at!
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Building a Better World in your Backyard by Paul Wheaton and Shawn Klassen-Koop