Ideally, you'll want some kind of hot-deployment support so that your users won't ever notice a service interruption. Common methods of achieving this are:
Having multiple instances of the web application behind some kind of load balancer which directs incoming requests to a running instance. If you'd perform a deployment, you wouldn't take all instances offline at once, but sequentially take one instance offline, redeploy, restart, and repeat this sequentially for all other instances.
Code-based hot-swapping while the software is running. The Oracle's JVM has limited support for this (HowSwap). A popular commercial tool which enables redeployments (using more sophisticated mechanisms than HotSwap) of Java web apps is LiveRebel.