What started as an inquiry about some of the more subtle aspects of Assassination is slowly turning into a resource for advanced tips and tricks. To let everyone utilize this more efficiently I've decided to turn the thread into a Q&A and use the most commonly agreed upon inputs as answers. A word of warning though: many of the answers are based on preference and experience, and haven't been confirmed mathematically. I therefore encourage you to take them with a grain of salt and sip through the replies to reach Deep Insight.
Rotations & Priorities
Q: What's the best opener as Assassination in 5.2?
A: Mut > SnD > Shadow Blades > Mut > Rupture > Vendetta > Standard Rotation. [1,2]
Q: What rotation should I be using on multiple mobs?
A: 2-3 targets: 2x Muti > Rupture. Repeat this cycle on all targets while weaving Envenom to maintain SnD. FoK spam during Envenom.
A: 5+ targets: 2x FoK > Rupture. Repeat this cycle on 3 targets while weaving Envenom to maintain SnD. FoK spam during Envenom.
Q: I've got the standard rotation down, but what about all those special situations?
A: Refresh Rupture at any CP if it has <2 sec left.
A: Envenom at any CP if Slice and Dice has <2sec left.
A: If Rupture has 3-6 sec remaining and 5 CP for Envenom, wait for the 2 sec mark and refresh Rupture before continuing your rotation.
A: If at 1-4 CP, use Blindside proc right away. If at 5+ CP and no Envenom up, Envenom then Blindside.
Q: Envenom clipping?
A: Only clip if you're at 7 CPs (presuming Anticipation) or 85+ energy.
A: Up to 1 sec of Envenom carries over to the next Envenom, so you can safely clip within this time frame. E.g. if you clip with 0.9 sec left, your next full Envenom will last 6.9 sec, and it won't be a DPS loss. [1,2]
Q: Energy pooling - yes/no/when?
A: If your previous Envenom has not dropped wait until it does or until your energy is in danger of capping before casting the next one. 
A: Go into Shadow Blades/Vendetta with high (but uncapped) energy. 
A: Try to have enough energy that you will be able to cast two Mutilates during the buff before casting Envenom. 
Q: Is it a single target DPS increase to multi-Rupture?
A: In short: no. On top of the facing requirements and the need to maintain DP on the secondary target for Venomous Wounds to proc, it's effectively energy neutral. The only time you want to multi-Rupture on single target fights is to get more on-demand burst. 
Spells & Cooldowns
Q: Do you hold back Vendetta to align it with Shadow Blades?
A: Only hold back if you're sure you won't be able to use another Vendetta, e.g. with <=2min of combat left on the encounter.
Q: Why is no one using Garrote?
A: Garrote and Rupture both apply Venomous Wounds, but they don't stack, and Rupture ticks every 2 seconds compared to Garrote's 3 seconds, giving you less energy over time. Mutilate and Ambush - the two alternative stealth openers - both add two combo points, and hit harder. 
Q: Using Vanish on cooldown or aligning with CDs?
A: The damage boost of Vanish (presuming Shadow Focus) is around 1% - the bailout might be better, depending on the situation.
Q: To what extent are you timing abilities with procs (e.g. Dancing Steel and trinkets)?
A: If ICD on multiple procs is about to expire, hold back on the big cooldowns. Otherwise don't bother.
Mechanics & Stats
Q: Is item X or set bonus Y and upgrade over Z?
A: The answer is that it's individual. For any and all questions regarding item choices, gems, enchants and item upgrades, consult with the Holy Grail of rogue itemization: the Shadowcraft.
Q: How are DoTs affected by cooldowns and procs?
A: When you cast a spell like Rupture, it will take a snapshot of your current game state, e.g. trinket procs and cooldowns, and use that for every tick of the spell - even after those procs have faded. However, your target's buffs and debuffs interact dynamically with this - so when you cast Vendetta halfway through a Rupture, it will increase the damage of that spell as long as Vendetta is active.
Q: To expertise cap or not?
A: There seems to be some disagreements here, but the bottom line is this: going for 2.5% Expertise is a theoretical DPS increase, but puts your yellow attacks at risk of being dodged which can result in miss-managing cooldowns and abilities. If the latter becomes too much of a nuisance, reforge to 7.5% Expertise.
Q: Haste or mastery!?
A: The general rule of thumb is this: with 1 RPPM trinket, mastery is slightly better; with 2 RPPM trinkets, haste is slightly better; with 2 RPPM trinkets and Legendary Meta gem, haste pulls considerably ahead. Add to this that movement intensive fights favor mastery, and mastery tends to give more consistent output. As always, mileage may vary, so consult with Shadowcraft to be sure.