You can do the following:
standalone.xml:
<subsystem xmlns="urn:jboss:domain:naming:1.2">
<bindings>
<simple name="java:global/user" value="newUser"/>
</bindings>
</subsystem>
and in spring context:
<bean class="java.util.Properties">
<constructor-arg>
<map>
<entry key="user">
<jee:jndi-lookup jndi-name="java:global/user" />
</entry>
</map>
</constructor-arg>
</bean>
In your app configuration you can have things in ejb-jar.xml deployment descriptor like
<javaee:env-entry>
<javaee:description>JNDI logging context for this app</javaee:description>
<javaee:env-entry-name>logback/context-name</javaee:env-entry-name>
<javaee:env-entry-type>java.lang.String</javaee:env-entry-type>
<javaee:env-entry-value>our-app-context</javaee:env-entry-value>
</javaee:env-entry>
or, if you prefer to have it in the server standalone.xml, do
<subsystem xmlns="urn:jboss:domain:naming:1.1">
<bindings>
<simple name="my/jndi/key" value="MyJndiValue"/>
</bindings>
</subsystem>
the latter (standalone.xml) is a JBoss 7.1 feature, so available in EAP 6.0. In JBoss AS 7.0, a dummy application needs to be used according to this thread.
What if simply:
InitialContext ctx = new InitialContext();
ctx.bind("varName", "value");
If you use that code inside of a JBoss instance you can bind variables into jndi. Remember to use the correct format for varName to bind the variable in the desired scope.