"ant" tool from apache may be useful for ur purpose.
If u r using Visual Age then deploying EJB to Websphere is merely a cake walk for u.Try that
The latest specification for J2EE specifies that web applications 'd be bundled as .war file ur ejb in a .jar file and u can combine both of this to a .ear file.The files u can create using jar utility
Hope this will be of some help to u
Pramod