I\'m using maven 2.0.9 with Eclipse 3.3.2.
I\'m used to launching a fresh build once per day by a mvn clean install.
Then, if I refresh my Eclipse project,          
        
To solve this problem here is what I did:
-----------Cut below here for script--------------
/*
 * Menu: Find System Prints > Beanshell
 * Script-Path: /GroovyMonkeyScripts/monkey/UpdateMavenDerived_Beanshell.gm
 * Kudos: Bjorn Freeman-Benson & Ward Cunningham & James E. Ervin
 * License: EPL 1.0
 * LANG: Beanshell
 * DOM: http://groovy-monkey.sourceforge.net/update/plugins/net.sf.groovyMonkey.dom
 */
out.println("Setting target directories to derived status.");
var projects = workspace.getRoot().getProjects();
for ( var i = 0; i < projects.length; i++) {
    var project = projects[i];
    if (project.isOpen()) {
        out.println("Project: " + project.getName());
        var members = project.members();
        for ( var j = 0; j < members.length; j++) {
            if (members[j].getName().equals("target")) {
                out.println("setting derived status on: "+ members[j].getFullPath());
                members[j].setDerived(true);
            }
        }
    }
}
I had some issues because some solutions here only work for some views, so I made an illustrated summary.
Tested in Eclipse 4.4 (Luna), should work like this since 3.7 according to other answers here.
Package Explorer View Menu → Filters... →  check Name filter patterns and input target.
Be careful, this will hide all folders and files named target, not just the default maven build directory! The Project Explorer view has a better option without this issue.
 

Project Explorer View Menu → Custom View... →  search for "maven" and check Maven build folder.
Checking this option hides the build directory as defined in the projects pom.xml configuration.
 

Solution for Indigo [SR2]
Project Explorer > Customize View > Filters > [*] Maven Build Folder
Did you try configuring the "Java Element Filters" option dialog box, (through the top-right arrow of the project explorer) ?
If needed, you can define your own ViewerFilter
The maven plugin does not hide away the target directory. It does however use the maven target folders to configure eclipse. So target/classes and target/test-classes are used by eclipse, and eclipse filters these folders out. This is done by "mvn eclipse:eclipse" as well as by the m2eclipse plugin. What is left visible is everything in the target directory besides these two folders (the generated jar file for example).
You can create a filter for the package explorer, but that will not influence the "open resource".
Reconfigure "clean" in Maven not to delete target directory:
<plugin>
    <artifactId>maven-clean-plugin</artifactId>
    <configuration>
        <excludeDefaultDirectories>true</excludeDefaultDirectories>
        <filesets>
            <!-- delete directories that will be generated when you 
                 start the develpment server/client in eclipse  
            -->
            <fileset>
                <directory>target</directory>
                <includes>
                    <include>**/*</include>
                </includes>
            </fileset>
        </filesets>
    </configuration>
</plugin>
(found at: http://maven.40175.n5.nabble.com/how-to-NOT-delete-target-dir-td3389739.html#a3413930)