You have to care about the classpath but also about the build.properties. If it is not part of the build properties, the libraries will not be part of the generated *.jar file.
Let assume that your plugin is named 'rts.core.libs' and the project includes a folder named 'native/dll'.
Your file .classpath will look like
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins">
<attributes>
<attribute name="org.eclipse.jdt.launching.CLASSPATH_ATTR_LIBRARY_PATH_ENTRY" value="rts.core.libs/native/dll"/>
</attributes>
</classpathentry>
<classpathentry kind="src" path="src"/>
<classpathentry kind="output" path="bin"/>
</classpath>
and your build.properties file looks like
source.. = src/
output.. = bin/
bin.includes = META-INF/,\
.,\
native/