Marks Hunters shot rotation/priority is:
Hunters Mark, rapid fire, kill shot, serpent sting, chimera shot, aimed shot, and spam steady shot until one of the other shots is off global cool down. You can add arcane shot in the roation but it depends on your talents and gear. The only time you should need to re-apply serpant sting is if it fails to re-apply with chimera or it just comes off due to the fight.
If your the only hunter always make sure Hunters mark is up, if you have another hunter you need to ask if they have Improved Hunters Mark (or just inspect them) and if they have more points into it then you, they need to make sure theirs is up, your's will over ride the IHM and you don't want to reduce the bonus from theirs. I run with another hunter but he is survival when we raid so I always make sure my mark is up on fights.
True shot aura is also over-ridden when you have a dps death knight or an enchancement shaman, so if you raid with a dk you can drop the point in TS and place it else where.
Your talent tree will also make a difference, points into brarrage and silencing shot (silencing shot only does 50% weapon damage and most bosses you can't silence) are a waste (let the mages and locks do the aoe damage on trash mobs) and place the points into talents that will help on boss fights.
Also, your DPS will change depending on the boss fight and your role in the fight, fights like the Lich King has a ton of movement, miss-directs and tranq shots and will reduce your damage done.
