(barring killing the left Rakghoul first, though I'm sure someone, somewhere swears by it since it's got the highest damage of the lot);.
While I personally prefer to take out the Commander first (I play Tank, MDPS and RDPS) because as a tank I value control over the fight above all else. That being said I understand the reasons behind the other strats, but since you mentioned killing the left rakghoul first, there is an interesting strategy I ran with one group when I was playing my sniper.
They claimed that if you killed the left guy first, the pin of the big guy became just a minor annoyance, afterall, the majority of the damage that comes from the pin is the Sword guy coming up and smacking you. Surprise surprise the kill order worked just as well as the other two kill orders.
I do remember when the flashpoint first came out, and I remember running it on hard mode for the first time (group was a good mix of Columi and tio equivelent). We wipped quite a few times leading up to the final encounter but actually managed to one pull the boss using a commander first, sword guy second and actually killing the big guy last (We kill the big guy second now though).
Different strokes for different folks really, all in all I just go with whatever strategy the tank is most comfortable with.