Default Talents - Shadow Focus is your best friend for the opener and really utilizing ambush in your rotation. I personally never change this talent unless I'm PvPing.
Anticipation - Overall best way to utilize shadow blades and seal fate procs never losing a combo point

Glyph - Glyph of Vendetta is best for targets that you will remain on for the full 30 sec duration. Anything less and you’re better off with replacing it.

As a rogue we should really be helping out our other DPS with Tricks of the Trade. Sacrificing your 15 energy for +15%/6sec dmg to your top DPS is insanely helpful. Strongly recommend utilizing this into your rotation.

Make this quick and painless. Here are my recommended Talent and Glyphs for each fight.

Immerseus: Talent: Cheat Death or Elusiveness & Burst of Speed. Glyph: Feint
(Feint helps the healers out tremendously on the add phase raid aoe.)
Also, depending on raid DPS you can remove Vendetta especially since the health pool is drained over time.

Fallen Protectors: Talent: Cheat Death, Shadowstep Glyph: (REMOVE: VENDETTA) ADD: Redirect, Sprint and Cloak.

Norushen: Talent: Cheat Death/Elusiveness, Shadowstep and Paralytic Poison. (If you are not one chosen to go into the add realm and are given add duty Marked for Death would be a great option. ) Glyph: Redirect (add duty: Kick, Cloak and Remove Vendetta)

Sha of Pride: Talent: Cheat Death/Elusiveness Glyph: Sprint, Smoke Bomb, Sharpened Knives & Vendetta

Galakras: Shadowstep, Prey on the Weak. Glyph: Redirect, Sharpened Knives, Smoke Bomb & Safe Fall

Iron Juggernaut: Talent: Cheat Death/Elusiveness, Shadowstep Glyph: Vendetta, Cloak, Feint
NOTE: Well-timed Shadowstep can negate the knockback from Shock Pulse. Pop Improved Cloak and soak crawler mines. Sprint glyph should not be needed with correct boss placement and well timed shadowsteps.

Dark Shaman: Talent: Cheat Death, Shadowstep. Glyph: Vendetta, Redirect, Cloak
Note: Cheese Strat you won’t need redirect. Two tank strat use redirect to keep your rupture up on both bosses.

General Nazgrim: Talent: Combat Readiness, Cheat Death, Shadowstep, Prey on the Weak. Glyph: Vemdetta, Redirect, Smoke bomb.

Malkorok: Talent: Cheat Death, Burst of Speed. Glyph: Smoke Bomb, Vendetta, Feint
Note: Always use your cloak when removing the Displaced Energy debuff. Your healers won’t have to worry about you.

Trash of Pandaria: Talent: Shadowstep/Burst of Speed, Paralytic, Marked. Glyph: Redirect, Sprint

Thok: Talent: Burst of Speed, Deadly Throw, (Shuriken Toss to play it safe on Phase 2) Glyph: Sprint, Smoke Bomb, Feint

Seigecrafter Blackfuse: On Boss -> Talent: Cheat/Elusiveness, Burst of Speed, Anticipation. Glyph: Sprint, Vendetta, Cloak
On the Line -> Talent: Burst of Speed, Anticipation. Glyph: REMOVE: VENDETTA ADD: Sprint

Paragons of the Klaxxi: Talent: Cheatdeath/Elusiveness, Shadowstep, Smokebomb Glyph: Redirect, Cloak

Healscream: Talent: BoS, Anticipation, Elusiveness/CD Glyph: Vendetta, FoKnives, Kick, Feint of using Elusiveness.
Note: Elusiveness really helps your healers on mini zone phases when Hellscream is casting Annihilate. With the added feint glyph you wont be missing too much energy and be able to focus more on boss.