What are the recommended plugins for eclipse to work with weblogic? Specifically I would need to work with older version of weblogic, 8.1, however I could use any version of Ecplise. I would like to debug the application and set breakpoints etc.
My bigger task is to move the project over to Jboss, can I deploy the same app on both app servers within Eclipse with presumably 2 sets of config files etc, any advice? 2 separate projects?
In order to debug your code running on Weblogic (or any other java server for that matter) you don't need anything but Eclipse itself. Search Google for java remote debugging.
As for deploying to Weblogic and Jboss - as long as your code is not using proprietary stuff from J2EE containers vendors you should be fine with one project. Standard configuration files will be common, container specific files will be separate and often won't even have to be removed in build time as container would just ignore them. This way the same artifact (e.g. War) could be deployed to both containers.
This concerns the JBoss part of the question: If there are real product-specific differences in the code, they should hopefully be localized to one or few classes. Apart from this hygienic measure, it would be unhelpfully painful to separate your project into two.
Most of the configuration files should be the same for the two environments too; if not, you may consider doing what we do at my job site: We have a conf_XXX and a conf_YYY directory for separate configuration files.
The problem of including/not including the correct files per deployment environment should be delegated to one or two ant build scripts. If there are indeed file differences, you can create a proj_Weblogic.war and a proj_jboss.war and deploy those to the appropriate servers. If you can't find specific deployment ant tasks, you can still use straight file copy tasks or scp to move your WAR files into the server's appropriate deployment directories.
This is easy with IntelliJ. No plugins needed - it's built in. I'd recommend junking Eclipse and trying a better IDE.
If you are using Eclipse with the WTP, then Weblogic Integration is available through an additional server adapter. To get it, right-click the Servers view then select New > Server and click on Download additional server adapters. Select the Oracle extension from the list and proceed with the install. Once installed, you'll be able to add a new server for WebLogic from version 8.1 to 11g (for BEA WebLogic Server v8.1, look under BEA System, Inc.).
If you have WTP servers created for JBoss and WebLogic, it's definitely possible to deploy and run the same project on both of them, there is nothing particular to do (the proprietary deployment descriptors can coexist if you want to use them, you don't have to create 2 projects for this).