I use eclipse 2.1.3, have you gone to Windows -> Preferences and clicked on Tomcat ?? I don't know what Eclipse 3 looks like there, but in 2.1.3 i selected a project to use for my tomcat classpath.
Additionally if you right-click your project -> Properties click tomcat and in 2.1.3 you can say this is a Tomcat project.... order may be important here ;) e.g. i gave reverse order i think. Dave Been