Is it possible to create an "uber" jar containing the project classes and the project dependencies as jars with a custom manifest file?

Actually, I didn't check what the maven-shade-plugin is doing exactly (or any other plugin) as maven 2 has everything built-in to create a megajar or uberjar. You just have to use the maven-assembly-plugin with the predefined jar-with-dependencies descriptor.

Just add this snippet to your pom.xml to customize the manifest:

<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-assembly-plugin</artifactId>
  <configuration>
    <archive>
      <manifest>
        <mainClass>my.package.to.my.MainClass</mainClass>
      </manifest>
    </archive>
  </configuration>
</plugin>

And the following command will generate your uberjar:

mvn assembly:assembly -DdescriptorId=jar-with-dependencies

But, again, the default behavior of this descriptor is to unpack dependencies (like the maven-shade-plugin). To be honest, I don't get why this is a problem but, if this is really not what you want, you can use your own custom assembly descriptor.

To do so, first, create your assembly descriptor, let's say src/assembly/uberjar.xml, with the following content:

<assembly>
  <id>uberjar</id>
  <formats>
    <format>jar</format>
  </formats>
  <includeBaseDirectory>false</includeBaseDirectory>
  <dependencySets>
    <dependencySet>
      <unpack>false</unpack>
      <scope>runtime</scope>
      <useProjectArtifact>false</useProjectArtifact>
    </dependencySet>
  </dependencySets>
  <fileSets>
    <fileSet>
      <directory>${project.build.outputDirectory}</directory>
      <outputDirectory>/</outputDirectory>
    </fileSet>
  </fileSets>
</assembly>

Then, configure the maven-assembly-plugin to use this descriptor and to add the dependencies to the Class-Path entry of the manifest:

<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-assembly-plugin</artifactId>
  <configuration>
    <descriptors> 
      <descriptor>src/assembly/uberjar.xml</descriptor>
    </descriptors>
    <archive>
      <manifest>
        <mainClass>my.package.to.my.MainClass</mainClass>
        <addClasspath>true</addClasspath>
      </manifest>
    </archive>
  </configuration>
  <!--
  <executions>
    <execution>
      <phase>package</phase>
      <goals>
        <goal>single</goal>
      </goals>
    </execution>
  </executions>
  -->
</plugin>

Finally run mvn assembly:assembly to produce your uberjar.

Optionally, uncomment the executions element to bind the assembly plugin on the package phase (and have the assembly produced as part of the normal build).

OneJar has a maven2 plugin.

I've used FatJar for this in the past. http://fjep.sourceforge.net/

I had created a relatively simple application, the client was going to want to double click on an executable and have it just work. Installers or dependencies are out of the question. Fatjar bundled up the project libraries and referenced files from Eclipse into a several megabyte executable jar for me. Flawless.