Okay,
Stat prio (PVE) :
Before going through, I just wanna say that having a bit of everything is usually better in PVE than stacking only one or two secondary (outside of healers' Masteries). As in, getting around 10 % Vers even if not needed can outweigh an extra 12% Crit in terms of DPS increase for instance (and the damage mitigation is always neat)
DK : Mastery is a good stat for every spec, go for some Haste rune regen is slooooow otherwise especially on Blood, don't really have a magic number but 20% should be good. Vers is really useful too but so is Crit. DK's issue is that is want everything but can't have enough to be worth it. To make a comparison, Enhance also wants everything but can get to a truly efficient balance (see lower). Tbh if you pick DK, be ready to suffer more than most classes no matter your secondaries (but damn what a cool class)
DH : Vengeance wants to go Crit/Haste, 30% Crit and 25% Haste, get Ele force on Heirlooms/Artifact, it's better than one WF weapon and I would argue for it being also better than 2 WF weapons in single target. A bit of Vers for overall damage increase. Mastery is only useful for the talent making it increase your speed, 30 to 40 Mastery Rating grants around 10% speed increase I believe. Havoc needs Ooze for soloing, other than that, maybe trade a bit of Crit/Haste or Vers for Mastery.
Druid : Guardian wants Crit (at least 30%) and Mastery (as much as you can fit), a bit of Haste (around 15% is neat) and maybe some Vers if you want (5-10% max), back in SL we used to go full crit because non-crit heals were offset by the damage taken during cast. Feral will trade a bit of Mastery or Vers for more Haste (22-25% is okay). Resto wants Crit and Vers and I like having at least 20 % Haste on casters, Mastery isn't too useful for soloing. Don't really play Balance, can't say.
Hunter : Surv is Crit/Mastery->Haste (once again I like 20%) and Vers is by far the least useful secondary for Hunters. MM is Mastery/Crit->Haste (get some, you won't regret it) and Vers. BM would be Crit/Haste/Mastery->Vers, if a more experienced BM player can tell which secondary is better please tell, never been much of a BM hunt fan myself.
Mage : Arcane wants Mastery, Crit and Haste. Can't give precise numbers, Mage is kinda meh anyways. Other specs can't solo, Fire is great for questing tho.
Monk : Brawmaster loves Crit. Get a lot of it, you can afford it as litteraly no other stat is as good. Get some Mastery, 15% Haste and some Vers. But Crit is good, go for that 35% (then having other secondaries is better). The other specs want more Haste.
Paladin : Prot is Crit->Vers/Mastery->Haste (get at least 15%), Ret is Crit->Haste/Vers->Mastery. Holy is Vers->Crit/Haste->Mastery (get some early on, you really need it when in low ilvl). Best is to go Prot during low ilvl and switch to Ret later on. Holy is fun but overall a worst Prot.
Priest : For Disc and Holy, Mastery is useless in PVE except maybe in early gearing. Go for maybe 10 to 15 % Vers and get a lot of Crit. 20% haste will do the job. Don't really play Shadow, can't say.
Rogue : ... Ooze... Other than this, go like DH and get Crit/Haste and a bit of Vers, Mastery is meh.
Shaman : Resto wants Crit/Haste/Vers. Mastery is useless (used to be BIS secondary in SL but now we're too strong for this) I'd say more or less 22-25% of each, maybe 25% Crit/Haste and 20% Vers. Honestly too bad Mastery is useless now, it is such a fun stat for RSham. Enhance litteraly enjoys everything. You'll want at least 25% crit, 20% haste and 50-60% Mastery. Then if you can get 10-15% vers (you prolly can) it's great. Ele is kinda like Enhance but stacking more Mastery is so fun
Overall Shaman have the most interesting Masteries (big-ass heals, Stormstrike and Windfury procs, double Lava Bursts)
Warlock : Kinda like Hunters, Vers is less interesting. Honestly all other stats are really good, forget Vers and get Crit on Destro.
Warrior : Prot is Crit->Vers/Haste->Mastery; Arms is Crit->Vers/Mastery->Haste, a bit more haste for Prot. I like having at least 20 % for Prot and 15% minimum for Arms. You could argue for less haste. I don't play Fury too much but I don't see a secondary clearly outweighing the others.
For weapon enchants, none is really gamechanging right now (BRING BACK ELE FORCE) go for whatever
I don't see any other dungeon quest than TBC, Classic ones have less secondaries, MOP ones are equivalent to WOD WF but can't proc socket/terts. Maybe Wrath quests can be interesting, I don't remember tbh.
On to races :
BIS is Tauren. No argument needed. Dwarves for Alliance.
On a more serious note, Tauren is really good (War Stomp, extra Stam is neat). Goblin has reduced prices, Rocket Jump and mobile Bank (neat). That said, PVE wise there is no clear BIS for Horde, maybe Tauren but Goblin is also good.
Night Elf is prolly BIS for PVE on Ally side (Shadowmeld basically), Human have the 10% rep boost for rep grinds. Dwarves have the best in-combat active racial (and the best facial hair) with Stoneform but if you want pure BIS it doesn't outweigh the benefits of Shadowmeld.
That said, play whatever you want, Bloodthorn Ring makes for a discount Shadowmeld anyways.
For gems BIS is SL gems on ilvl 87 for the speed and health regen (this one is for vets). During SL I was more of a +2 primary stat +2 stam guy. Now, with stam granting less HP 2 Stam went from +22 hp to +24 and now +16hp. As of 10.1 I think that the best non-SL gems would be the +2 primary stat +2 any secondary or the +3 primary stat.
Hope I answered your questions, have a good one