Since so many people are asking, here is my setup for the routine when I PvE on my rogue. I've never been below 90th percentile on any fight, and I frequent 95-99th percentile, with one rank 5 parse as Combat. I've been raiding for a while, I've cleared mythic imperator and heroic blackhand and am currently progressing through mythic brf with this routine.
Combat settings:
Take off auto interrupt if the fight requires something specific to be kicked (IE if you are going up on the boat in Iron Maidens.) Notice I don't run any Cooldowns on burst, and I have the routine pause for a moment if I manually hit a button. Use EVERY cooldown manually for optimal dps as combat. Use vanish whenever you don't have enough energy to cast anything else. Use Adrenaline Rush on cooldown as long as you'll have 100% uptime on the boss (if you'll have to run to do a mechanic at any point during it, don't use it yet.) Use killing spree on cooldown as long as using it won't get you killed by a mechanic.
Advanced tips: Don't use killing spree unless you are low on energy, also keep track of your Guile Tiers. If you are one sinister strike from going up, it's usually worth saving a cooldown for that 1 sinister strike then popping it. You should always use an agility potion before the pull, and then preferably again during heroism. If the fight hero's at the start, use it about midway in the fight when your killing spree, adrenaline rush and trinket if you have an on-use one, should all be off CD at the same time again.
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Notice I don't let it manually use blade flurry. While it -can- notice areas to stand for maximum AoE that I normally wouldn't notice, it also turns it off the moment a target runs out of range, and on fights like Hans and Franz, Iron Maidens etc, if it turns it off every time someone runs away, it's going to be a dps loss. The bosses aren't apart for the full 10 seconds of the cooldown, so its best to just keep it on.
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For Sub - Use the exact same settings as above, just toggle Vanish Offensive on burst on page 1. I run all cooldowns on burst for sub because I'm lazy, and the routine does a pretty good job of using them at good times. The only fight I've experienced an issue on is Blackhand, on occasion it's popped Shadowdance right as we fall through the floor, but generally not a big deal compared to the dps increase it gives me over doing it manually (I do a bad job of keeping track of expose weakness / premeditation). If you are experienced with sub, you would probably find a dps increase using the CD's manually. (IE Noxe's sub guide recommends using Shadow Reflection at the start of the fight to get two ruptures off ASAP. This IS a dps increase, but the routine doesn't do this. Just one thing you can improve by doing it manually). Use your prepot once before the fight and again when your Shadow Dance, Shadow Reflection, and trinket if you have one are off cd again.
Assassination - I don't play this spec at all, as it generally parses lower than sub / combat this xpac, however if you are using it, I'm sure the above settings would work fine, and again I would recommend you learn to use your CDs manually.
Defensive cooldowns - As a raider, you should always be trying to minimize the damage you take. Use smoke bomb on melee whenever you are about to take large raid wide damage (Ie demolition on Blackhand.). Pop Cloak of Shadows whenever magic damage is about to fuck you up (ie using CoS prematurely on Ko'ragh when hes casting Fire Aura, will save your healers and melee a lot of heart ache.) Feint costs a lot of energy to use, so it's not recommended to be used mid fight often, but on fights like Oregorger, you can pop it right as he's about to slam into the wall during his roll phase, and you'll take a good deal less damage from his raid wide impact damage.
Glyphs and Talents :
Icy Veins - World of Warcraft News and Guides
Other notes : Sprint and Shadowstep are amazing, use them whenever the boss is on the move. He is generally going to run faster than you, because he only chases the tank once he leaves his hitbox (bosses have large hitboxes). Any second you aren't hitting the boss is a huge dps decrease. Don't be lazy about these, and don't forget about them.
LEARN THE BOSS YOU ARE FIGHTING. For example, Operator Thogar. Saving your killing spree for the first wave of adds is a dps increase over burning it immediately. Different fights may make you have to change your stategy a bit to get the most dps.
TL;DR - If you use these settings and then have a basic understanding of your class, you will parse just fine with this routine. Keywords for basic understanding if each spec. Combat : Ruthlessness (it's a passive. Look it up). Subtlety: Expose Weakness (It's a passive whenever you ambush, look it up). Assassination : I have no clue, if someone can fill me in, I'll edit this. Learn about those passives and work around them, you'll gain some dps.
update - For anyone wanting to increase their sub dps, I would recommend going to \Honorbuddy\Routines\TuanHARogueWoD\Settings - and under Rogue-Settings , find Hemorrhage and set it to false. Until Taunha pushes an update to not make it cast during Expose Weakness, its a massive dps loss. If you want, you can cast it manually whenever Expose Weakness isn't on for a minor dps increase.
(Turning it off gave me 3-4k extra dps on Gruul)