This is left up to Tomcat 6 to produce, and as such tomcat-6.x ebuilds likely need to be updated to not build this jar. el-api.jar should be part of tomcat-servlet-api as it is in 3.0 and 3.1. It is just missing from 2.5, and needs to be built and installed. While modifying tomcat-6.x to not build the el-api.jar, and use it from tomcat-servlet-api-2.5.
Fixed in 6.0.44-r1. I'll close this when stable.
(In reply to James Le Cuirot from comment #1) > Fixed in 6.0.44-r1. I'll close this when stable. Done.