When an application is installed in WebSphere Application Server (WAS), by default it is configured to start automatically whenever WAS starts. This document provides instructions on how to disable applications from automatically starting up when WAS starts up. Disabling application from automatically starting up accelerates the initial server startup.
From the Administrative Console:

From WSAdmin (Jacl):
Set appName Strategy
puts "Disabling auto load for $appName"
set deployments
set deploymentObject
set targetMappings 0]
$AdminConfig modify $targetMappings {{enable false}}
puts "Saving all the changes to master configuration of WebSphere..."
$AdminConfig save
Note: The script can be expanded to disable all applications through via and a loop. For more information on WSAdmin, refer to the following IBM WebSphere v6r0 document:
http://publib.boulder.ibm.com/infocenter/wasinfo/v6r0/topic/com.ibm.websphere.express.doc/info/exp/ae/txml_scriptingep.html