howard,
You need to manually check which jars are part of your project development and then remove the jars which are not required, from the java build path or WEB-INF/lib folder.
You can use user libraries in MyEclipse. Right click on your project > Build path > Add Library. This would open Add Library wizard. You can select “User Library” and follow the wizard. These libraries get added to your project build path. These user libraries created can be added to any projects in your workspace.
Alternatively, can you please check Tomcat shared library files mechanism where we store all the jar files in the tomcat directory and make them visible to all installed web applications. Please look at this link for more information – http://tomcat.apache.org/tomcat-7.0-doc/appdev/deployment.html#Shared_Library_Files
Hope this helps.