How to use a List of arrays in Java?

Why not declare your own class for a point? e.g.

class Point3D {
  int x, y, z;

  public boolean equals() {
    // logic
  }
}

and then declare List<Point3D>.

A general solution is to wrap the array in a method that does implement equals (and hashCode and perhaps compare, possibly toString and other methods that might make sense) as you wish:

public final class IntArrayWrapper {
    private final IntArrayWrapper[] values;
    public IntArrayWrapper(int... values) {
        if (values == null) {
            throw new NullPointerException();
        }
        this.values = values;
    }
    @Override public boolean equals(Object obj) {
        if (!(obj instanceof IntArrayWrapper)) {
            return false;
        }
        IntArrayWrapper other = (IntArrayWrapper)obj;
        return java.util.Arrays.equals(this.values, other.values);
    }
    @Override public int hashCode() {
        return java.util.Arrays.hashCode(values);
    }
    public int[] getValues() {
        return values;
    }
    [...]
}

In this specific case, using arrays to contain certain fixed data values is poor design. Do it properly:

public final class Point {
    private final int x;
    private final int y;
    private final int z;

    public static Point of(int x, int y, int z) {
        return new Point(x, y, z);
    }
    private Point(int x, int y, int z) {
        this.x = x;
        this.y = y;
        this.z = z;
    }
    @Override public boolean equals(Object obj) {
        if (!(obj instanceof Point)) {
            return false;
        }
        Point other = (Point)obj;
        return
            this.x == other.x &&
            this.y == other.y &&
            this.z == other.z;
    }
    @Override public int hashCode() {
        int hash;
        hash = x;
        hash = hash*41+y;
        hash = hash*41+z;
        return hash;
    }
    [...]
}

First of all, this isn't legal syntax. List can only take a single generic type.

Second, I would say that if you're worried about doing things at this low a level you aren't thinking abstractly enough. An array of arrays or a List of Lists is common enough. People who create matrix classes for linear algebra use them all the time. But you leverage objects and Java best when you hide those implementation details from clients of your class. Try it for your case and see if it helps.

You could always use the existing Point3d class instead of an array.

edit: The Apache Commons Math library also has some good options.