For our 2-pilot crew part 121 flights, I do not, nor do I know ANYBODY who would EVER log PIC while acting as SIC. The only benefit you will get from logging "sole manipulator" PIC time in airline flying is a little bit of petty ego gratification while looking at an inflated number in your logbook. Any major airline interviewer who finds that half of your 737 or 767 F/O time was logged in the "PIC" column will not be comparably impressed. The "sole manipulator" rule is legitimately applied while flying empty legs in a Part 91 corporate type environment, or logging PIC while receiving dual instruction for your ATP or CFI certificate (since the CFI is likely also logging, and acting as, PIC).
For our 3 pilot crew flights, under the new FAR part 117 EVERYONE logs the ENTIRE flight under "total duration of flight", even while on break (see the ALPA guide to Part 117, scroll to question "Q-51":
http://www3.alpa.org/portals/alpa/co...quirements.pdf). The designated Captain logs PIC the ENTIRE time, and the FO and IRO log SIC. The theory is that you are all REQUIRED to be there to make the Flight Duty Period legal, even if you are asleep at a given moment. So you log total duration, and your designated position for the entire flight time. You obviously don't log actual instrument time while you are asleep. Common sense.
In essence the IRO sitting in the left seat relieving the Captain is doing so under the Captain's instructions, therefore he is still SIC. The FO in the right seat at this point is really considered "third in command" but since there is no such term, he logs SIC too. Part of the crew-change briefing includes the Captain telling the IRO (who is taking the left seat) how he would like the flight conducted, and what kinds of things he wants to be woken up for. If anything really important or non-routine comes up, the final decision still comes from the Captain, unless it is of the immediate life-and-death variety. So the Captain still "commands by delegating" from the bunk, hence logs PIC while the other two log SIC.
To deepen the discussion, sometimes when we are short FOs for whatever reason, the IRO position is staffed with a line captain. We also have ULH flights with 4 pilot crews using 2 captain and 2 FOs. Even in those instances, the only person who should be logging PIC is the captain that signs the flight plan, ALL other crewmembers are acting as, and logging, SIC.
If you signed your name to the flight plan under part 121, log the whole thing as PIC. If somebody else signed their name to the flight plan under part 121, log the whole thing as SIC. You will NEVER get in trouble and your logbook will NEVER be questioned if you do this.
If sole manipulator or PF time matters to you for any particular reason, do as the others here suggest and log it as such in a separate column that does not contain the word "PIC".