If you often have to create new application servers, you should consider application server templates: http://www14.software.ibm.com/webapp/wsbroker/redirect?version=compass&product=was-nd-mp&topic=trun_create_templates
The process is simple: create one application server, add your customizations (JVM arguments, data sources, etc.), then click Templates... > New, and select that server. Starting in WAS 7, you can even edit the template after it has been created. Then, when you create a new application server, either through the console or wsadmin, choose the template you just created.
Any changes you make to a template do not affect servers previously created with that template. This function is available in WebSphere Virtual Enterprise with the dynamic cluster template: http://publib.boulder.ibm.com/infocenter/wveinfo/v7r0/topic/com.ibm.websphere.virtualenterprise.doc/odoe_task/todrdynamiccluster.html
If you want to do something like this in Network Deployment, then I would recommend using wsadmin Jython scripts to apply "template" changes to your servers. You can base your scripts off of the script libraries available since WAS 7, such as iterating over servers, adding properties, etc. You can also use the job manager, available since WAS 7, to centralize this administration. Scripting all of your administration is also the recommended way to administer a multi-call, hot backup, continuous availability solution: http://www.ibm.com/developerworks/websphere/techjournal/1004_webcon/1004_webcon.html