Whichever way you go, realize the following.
When desiging a web app as you have described, it is ALWAYS better to use a pool. I suggest that you ALWAYS get that pool from JNDI as a javax.sql.DataSource object. Many, many other APIs, tools and products are designed to work with either a java.sql.Connection or a javax.sql.DataSource. You use web.xml to define the name of the DataSource you want (via a <resource-ref> tag) and your code is good to go.
All that gives you is a .war file that fits the standard. Your code will use an existing DataSource, but not configure one. The configuration of the DataSource is done one of two ways. In a server specific way, you define a DataSource. With tomcat this is done in the server.xml file (last I checked anyway). With many other
J2EE servers, there is a GUI to do this (there may be one with Tomcat now). Tomcat does use the Jakarta Commons classes to do this. The other way is to have your app create the connection. This is not recommneded, but once the DataSource is up and running, it works the same way.