I think you probably don't want an each function unless you increment a delay or something in it. The animate method has a callback which will call a function on completion of the animation (the 4th parameter). So you can make it recursive like this...
var rsr = Raphael('rsr', '600', '300');
var fillColor = {fill: '#00A651','stroke-width': '0','opacity': '1'}
var circle_b = rsr.circle(513, 128, 4).attr(fillColor);
var circle_c = rsr.circle(477, 128, 4).attr(fillColor);
var circle_d = rsr.circle(441, 128, 4).attr(fillColor);
var circle_e = rsr.circle(406, 128, 4).attr(fillColor);
var circle_f = rsr.circle(370, 128, 4).attr(fillColor);
var circle_g = rsr.circle(334, 128, 4).attr(fillColor);
var circle_h = rsr.circle(298, 128, 4).attr(fillColor);
var circle_i = rsr.circle(262, 128, 4).attr(fillColor);
var circle_j = rsr.circle(226, 128, 4).attr(fillColor);
var circle_k = rsr.circle(191, 128, 4).attr(fillColor);
var circle_l = rsr.circle(155, 128, 4).attr(fillColor);
var collection = [
circle_b, circle_c, circle_d, circle_e, circle_f, circle_g, circle_h, circle_i, circle_j, circle_k, circle_l
];
function nextAnim( count ) {
if( count >= collection.length ) { return }
collection[ count ].animate( {'opacity': '0'}, 1000, 'linear', nextAnim.bind(null,count+1 ) );
};
nextAnim(0);
jsfiddle here