This week's book giveaway is in the OCMJEA forum. We're giving away four copies of OCM Java EE 6 Enterprise Architect Exam Guide and have Paul Allen & Joseph Bambara on-line! See this thread for details.
Stop thinking about the tools. Start thinking about the solution you are developing instead.
You want to deploy either an ejb-jar file, an ear file or a war file.
You want to be able to create one of those files in an IDE independent manner.
Your chosen solution should be such that if you give your source code to someone that doesn't have eclipse they should be able to generate an identical ear/ejb-jar/war file.