You can specify these parameters via context or environment parameters, such as in context.xml. See the sections titled "Context Parameters" and "Environment Entries" on this page:
http://tomcat.apache.org/tomcat-5.5-doc/config/context.html
As @netjeff points out, these values will be available via the Context.lookup(String) method and not as System parameters.
Another way to do specify these values is to define variables inside of the web.xml file of the web application you're deploying (see below). As @Roberto Lo Giacco points out, this is generally considered a poor practice since a deployed artifact should not be environment specific. However, below is the configuration snippet if you really want to do this:
<env-entry><env-entry-name>SMTP_PASSWORD</env-entry-name><env-entry-type>java.lang.String</env-entry-type><env-entry-value>abc123ftw</env-entry-value></env-entry>