Eclipse allows you to refer to project B in project A's build path, doesn't it? So set up a project which just contains the commonly-used jars, and have all your other hundreds of projects refer to it.
Projects like what you're describing a usually very complex, and Eclipse isn't really intended to build complex projects all by itself. You're usually better off using Maven or Ant along with Eclipse.
Ant support is built-in, but Ant cannot fetch external libraries without help. Maven, on the other hand, is primarily based on the concept of external libraries (dependencies). You have to install an Eclipse plug-in to get full Maven support in Eclipse, but if you do, it will not only help you build those projects, it will automatically add the Maven dependencies to the Eclipse project build path.
An IDE is no substitute for an Intelligent Developer.