Here's how it works. BM hunters follow the same gemming progression as anyone else. However, we gain more benefit from gemming from Armor Pen earlier than either Marks or Survival hunter and continue to gain more benefit from it, even if our spec underperforms due to lack of pet scaling. The reason for this is that we do not have a special "shot" like chimera or explosive shot. The meat and potatoes of our damage comes from auto shot and steady shot, both completely physical attacks that benefit a lot from ArPen. If a BM hunter has I think it's greater than 540 ArPen passively - that's straight off gear, not with trinket procs active or enchants, gems, or stat food added - then he's good to start gemming for Armor Penetration. The reason a BM hunter does not want to gem haste is that due to Serpent's Swiftness, we are quite close to the haste cap through talents alone. Add to that what's on some of the more desirable pieces of gear already, and we need no further Haste tacked on. And it is true that as a BM hunter's gear improves, the pet becomes less of their overall damage and the hunter himself provides more of it. That's supposed to happen, unfortunately. It's the other reason that BM as a raiding spec underperforms...90% of our talents buff our pets, which don't scale, etc. I'm keeping my fingers crossed that this will be fixed in Cataclysm.
However you spec, gem, or enchant, if your DPS is acceptable to your raid, then you're fine.
For reference, here's my armory link (and I'll hope I didn't in fact log out still wearing RP gear. I know I don't have my raiding arrows equipped):
http://www.wowarmory.com/character-shee ... eathermoon
When I raid, I bring my devilsaur Clayburn. I will sometimes switch to my wolf on the Dreamwalker fight, simply due to the fact that there's some of those adds you just can't send a pet in on, so the wolf's howl does me better in that particular instance than having Clayburn who can't attack at all.