I booked through VS.com back in December for January 2009 travel on LHR-EWR and EWR-LHR. The LHR-EWR leg had a codeshare number and I was credited miles without a problem. The EWR-LHR leg no longer had a codeshare since CO18 was introduced and CO would not credit me the miles. (Which is quite frustrating since VS18 gets you in early enough to make onward connections at LHR but CO18 forces you to overnight.)

Of course, as with all things, YMMV.