Looks like Java appends to %path% its own paths. Nothing else.

If you're using Java 8, you can use StringJoiner.

/**
 * JEcho writes any command line argument to the standard output; each argument
 * is separated by a single whitespace and end with a newline (you can
 * specify '-n' to suppress the newline).
 *
 * This program doesn't interpret common backslash-escaped characters (for
 * exampe '\n' or '\c').
 */
public class JEcho {
    public static void main(String[] args) {
        boolean printNewline = true;
        int posArgs = 0;

        if (args.length > 0 && args[0].equals("-n")) {
                printNewline = false;
                posArgs = 1;
        }

        StringJoiner outputBuilder = new StringJoiner(" ");

        for (; posArgs < args.length; posArgs++) {
            outputBuilder.add(args[posArgs]);
        }

        String output = outputBuilder.toString();

        if (printNewline)
            System.out.println(output);
        else
            System.out.print(output);
    }
}

@Adi Tiwari, I've found the cause. Runtime.getRuntime.exec() doesn't execute a shell command directly, it executes an executable with arguments. "echo" is a builtin shell command. It is actually a part of the argument of the executable sh with the option -c. Commands like ls are actual executables. You can use type echo and type ls command in adb shell to see the difference.
So final code is:

String[] cmdline = { "sh", "-c", "echo $BOOTCLASSPATH" }; 
Runtime.getRuntime().exec(cmdline);

| needs to be interpreted by a shell.

String[] cmd = {"bash", "-c", "echo 'obase=94; 100' | bc"};

If you pass the string

Copyecho "A B C D E F G H I" | java Subset 3

as the command line arguments in Eclipse, you get the behavior you see. If, however, you enter this on the command line, the shell handles the command first. The shell interprets this as

1. Echo the string '"A B C D E F G H I"' to stdout
2. Launch a separate process to run the Java JVM, with arguments Subset 3
3. Pipe the stdout from the echo to the Java process' stdin

Then the JVM gets the arguments (Subset 3) and interprets the first string Subset as the classname to run and 3 as the arguments to the Java program.