JBossAS and JBossEAP support the same specifications.
But JBossEAP will be more stable. It is the platform for the JBoss support and significant JIRA bugs will be fixed with cumulative patches.
The EAP will follow more strict the JavaEE specifiaction.
Also the JBossEAP versions might be longer maintained as JBossAS versions.
JBossAS distribution might include new (instable) features or beta versions of upcomming changes.
If a patch is needed for this version you have to patch the source version according to the JIRA and compile your special JBoss version.
The "standard" configuration (that is, server/standard) in both EAP and AS conform to the Java EE specificartion, I believe that both are run against the compatibility kit.
EAP 5 is pretty much AS 5.1.0.GA + Seam + various fixes + various config changes (security lock-down) and a lot more testing.