With the sample builds taken from Shandara's Spreadsheet, with current best gear, in patch 3.2, it is clear that in theory, Marks is the best PvE DPS followed by Survival which is followed by Beast Mastery.
Marks (7/57/7) - 9289 DPS
Survival (0/15/56) - 8884 DPS
BM (54/12/5) - 8604 DPS
That is about a 7% difference between the lowly BM Hunter and the mighty Marksman Hunter. I would prefer if BM was within 5% of the top spec, be it Survival or Marks. BM may have the easiest rotation, but on pet unfriendly fights, it has the most to lose by far.
Talent DPS has changed most significantly (in patch 3.2) with Animal Handler. It used to provide 27 DPS per point (54 total). Now it provides 130 DPS per point (260 total). Just in that talent change BM Hunters gained 206 DPS (in my gear, spec, etc. on my BM page).
The Wild Hunt pet talent change increased a BM Hunters DPS by 137, but it also increases Marks and Survival pet DPS.
The expertise change for pets (Ranged Hit now gives Expertise for Hunter pets), is another area where our pets gained a bit of damage.
All in all, this is how my PvE pages total DPS has changed since 3.2 (again, with my gear, spec, etc.).
BM went from 6211 DPS before 3.2, to 6783 after 3.2. +572 DPS
Marks went from 6613 DPS before 3.2, to 6789 after 3.2. +176 DPS
Survival went from 6769 DPS before 3.2., to 6677 after 3.2. -92 DPS
Notice: My talent trees are not perfected for theoretical top DPS, as I usually forgo a couple of DPS talent points for Hawk Eye, as I tend to find that it adds unmeasurable DPS and longevity to my life in raids.
I'm not sure why my Survival build with my gear lost DPS from 3.2, but BM definitely gained the most since 3.2. In better gear, especially a better ranged weapon, Marksmanship would pull further ahead, like it does on the samples, as it scales better than BM (as does Survival).
My recommendation is to try out BM again if you have Naxx 25 / Ulduar 10 gear or less (it should be about equal to Marks DPS). But you might want to have a secondary spec as Survival or Marks in case you come across a pet unfriendly fight. If you have an Ulduar 25 or better weapon, your probably better off with Marks in PvE.