I'm not aware of the formatter being available this way.  The compiler
appears to be used in Jasper as distributed with Tomcat 5.5, so it is at
least possible to use it this way.

Mainly because you haven't packaged it that way yet.  Let's get back to
reality here!  There's no point acting like this is some big IBM
conspiracy to keep the functionality under wraps.  It's open source.  
Understandably, the project developers want to spend their time making
Eclipse better... and I'm quite grateful for that.  I think it's a wise
decision on their part.

In one of our projects I've used the Eclipse compiler to compile a batch
of Java files. This works perfectly. [Never used formatter stand-alone.]

You'll need the 'JDT Core' plugin: I've used org.eclipse.jdt.core_3.0.1,
in particular the class org.eclipse.jdt.internal.compiler.batch.Main in
jdtcore.jar. The following snippet shows how this class can be used

import org.eclipse.jdt.internal.compiler.batch.Main

/**
 * Compiles sourceFile and produces .class file in outDir.
 * @param sourceFile source file to compile
 * @param outDir directory of resulting class file
 * @return <code>true</code> if compilation was successful,
 *         <code>false</code> when compilation failed
 */
private boolean compileJavaSource(File sourceFile, File outDir)
{
  StringWriter javacOut = new StringWriter();
  PrintWriter pwJavacOut = new PrintWriter(javacOut);
  StringWriter javacErr = new StringWriter();
  PrintWriter pwJavacErr = new PrintWriter(javacErr);

  Main javac = new Main(pwJavacOut, pwJavacErr, false);

  String[] args = {"-d", outDir.toString(), sourceFile.toString()};

  boolean compiled = javac.compile(args);
  pwJavacOut.close();
  pwJavacErr.close();

  if (compiled)
  {
     // success
     return true;
  }
  else
  {
    // failed: log compiler messages
    __logger.severe("Java compiler stdout: " + javacOut.toString());
    __logger.severe("Java compiler stderr: " + javacErr.toString());
    return false;
  }
}