The only way I know of is to backup the entire workspace - your project's data is in the project's directory, and there is probably also a Servers directory which contains the Tomcat config info, and then I image that there is other information available in the workspace/.metadata directory. Backup up the Tomcat directory might also be a good idea, unless you don't mind rebuilding it.
By the way, you should really provide a better subject line for this topic, something like "Saving an Eclipse project"
A project and your Eclipse workspace are 2 different things. That's good, because you can archive out a project to a version conrtol system and someone else can import it even though their locations for support services such as the Tomcat server may not be the same (or have the same names).
But it does mean that you need to save your Eclipse preferences separately, since they're not stored in the project itself.
An IDE is no substitute for an Intelligent Developer.