Based on Jeremy's Gradle task (see https://gist.github.com/jeremyjarrell/6083207), but in pure Groovy. Can be integrated into a Maven build.

pom.xml

<plugin>
    <groupId>org.codehaus.gmaven</groupId>
    <artifactId>groovy-maven-plugin</artifactId>
    <version>2.0</version>
    <executions>
        <execution>
            <phase>package</phase>
            <goals>
                <goal>execute</goal>
            </goals>
            <configuration>
                <source>${pom.basedir}/prefixNewMigrations.groovy</source>
            </configuration>
        </execution>
    </executions>
</plugin>

prefixNewMigrations.groovy

import static groovy.io.FileType.*

def incrementalScriptsDir = new File("src/main/dbscripts");

/**
 * Traverses all files in the incremental directory, excluding the ones which already
 * start with a number followed by an underscore.
 * Each of these files will be renamed by prefixing them with a timestamp.
 */
incrementalScriptsDir.traverse(type: FILES, excludeNameFilter: ~/.+\d+_.*/) { file ->
    def timestamp = new Date().format('yyyyMMddHHmmssSSS', TimeZone.getTimeZone('GMT'))
    println "Renaming $file.name to ${timestamp}__$file.name"

    file.renameTo("$file.parentFile.absolutePath$file.separator${timestamp}_$file.name")

    sleep(1000)
}