Please keep in mind that for something like PvP specs or Glyphs, there is no “right” answer, especially regarding PvP Specs. There is a lot in speccing that comes down to preference, but hopefully these can serve as a general guide to what you hope to achieve.
This article is our compilation of the rogue specs that we feel are currently most viable as of 3.3. You can take this as a general guide and reference to specs than can work. PvE Specs are listed after PvP Specs.
Click on the links below for a look at the spec. I’m only listing Major Glyphs as minors are somewhat inconsequential, for PvE specs the Glyphs are included with the spec link as there is only one correct way to Glyph.
PVP SPECS
44 / 2 / 25
44 / 4 / 23
Glyph Options: Mutilate, Sprint, Vigor, Tricks of the Trade, Preparation, Cloak of Shadows
This is the most popular variation of the deadly poison arena spec which has become popular since the changes to master poisoner, and it has only gotten stronger since 3.3. For the most part this is the strongest arena spec for 3 v 3 at the moment. Deadly poison stacks very quickly with the improved poisons talent. This provides amazing wound dispel shielding, so abolish poison is a lot less of a counter. With this spec you now replace envenom with eviscerate, and the damage increase on plate and mail wearers will be very noticeable. It’s best to have a 1.4 speed offhand for this spec, and it’s very nice to also have a 1.8 speed offhand to swap to for rogue teams / openers if you intend to attack rogues, because this will provide much higher burst unless you get very lucky with deadly poison procs.
Talent Options - Alright, there are a ton of talent options here and there is no correct answer, it’s very situational. First I’ll talk about:
Heightened Senses and 2/5 dual wield vs. 4/5 dual wield: I see this as being a primary choice between increased damage and the ability to find stealth targets more easily. If your team is lacking on damage and you aren’t playing against many stealth teams, then 4/5 dual wield is probably the way to go. Also remember you will lose some rng survivability with 4 percent miss on spells and ranged from heightened senses. Both options can work, I’d say HS is more popular.
Imp Evis. vs Ruthlessness vs. Lethality: 3 points are free to go in any of these 3 talents. A lot of people pick up Imp eviscerate over ruthlessness or Lethality for situations when you want to do finishers but you don’t have enough deadly poison stacks. Generally Imp Evis is nice to have for swaps, it’s a good tool because without it you lose some burst for swaps. That being said, I think ruthlessness is a very underrated talent, because it allows for insane burst combos with 4 point finisher –> ruthlessness proc –> 1 mutilate gives you 4 cp –> 4 point finisher. The best potential of such combos at full energy can be huge. If one does choose to pick up imp. Evis, I personally would drop 3 in lethality over dropping 3 in ruthlessness. I also personally prefer the spec without imp. Evis because I think it’s far too situational in most cases to warrant the 3 point loss of lethality’s burst.
2/3 Deadened Nerves vs 2/3 Find Weakness: Your choice, damage vs. survivability. If you get focused a lot and die when that happens, you might want to go with deadened nerves. If you find your team is lacking a bit of damage on kill targets, go with find weakness. This choice depends a lot on the comp you are playing.
3/3 Initiative vs. 3/3 Serrated Blades vs. 3/3 Setup: I think initiative is the most popular choice here. It gives you a bit more punch off your opener and versatility when it comes to swapping. It’s nice to have. Your other main option here is serrated blades which is a raw damage increase, if your team doesn’t swap much it’s nice to have, and is of course better than initiative if you’re not landing openers. I’m listing setup here as well because it is an option, especially if you get focused by melee a lot, but it’s not a very popular one and is in my opinion the weakest of these choices.
Imp Ks: You can drop those points in find weakness or heightened senses and throw them here if you want, a good choice if your team does a lot of it’s burst during the kidney shot.
4x / 5 /2x
Glyph Options: Mutilate (this is a must have), Vigor, Tricks of the Trade, Preparation, Cloak of Shadows, Eviscerate
This remains one of the most popular PvP rogue specs. Having both quick recovery and deadly brew, combined with some of the best burst over time and long term damage is what makes this spec great. In comparison to deadly poison mutilate, you would want to run double wound / double 1.8 here for most situations. These spec shines against clothies / rogues, and is my personal preference for most dueling scenarios.
Talent Options - The basis of this spec is assassination down to mutilate and subtlety down to preparation and dirty deeds. This leaves you with 2 spare talent points. I find focused attacks is essential to the strength of this spec, so we see a choice between filling out find weakness, going 2/3 find weakness and picking up 2/2 Heightened Sense, or putting 3/3 find weakness and putting this talent elsewhere. You could also put these points into deadened nerves if survivability is a problem. This comes down to preference. Also, you can choose to pick up ruthlessness, either by dropping HS, focused attack, even find weakness or deadened nerves.
20 / 0 / 51
Glyph Options: Shadowdance (this is a must have), Vigor, Tricks of the Trade, Preparation, Sprint, Eviscerate
3.3 dance is kind of a forgotten spec, and likely sub will continue to be the forgotten tree until it gains access to some poison talents or some serious changes are made. Still, it isn’t completely useless as dance can generate some interesting options and shadowstep is always nice to have. Here’s the spec I would go with if I was playing shadow dance.
Talent Options - I personally would not play this spec without lethality, but it is optional. You could change a ton of things here, you could get 
imp gouge, you could drop points in deadliness for master of sub, move out of heightened senses, play without cheat death if you max out PvE gear. There are a lot of options here, and no real right answer. I’d suggest experimenting with a few until you find your niche. You can also choose between HS and 4/5 deadliness.
Thought I’d throw in this spec Unmercey linked to me as well. This is for those of you who miss the days of BC hemo+shadowstep PvP. You can certainly pull off some significant burst in a cheapshot after shadowstep with cb evis, especially as an engineer.
PVE SPECS
I’m sure there are other competitive PvE options out there but for now I’ll focus on what I believe to be the top choices for maximum damage output.
(the best glyphs are including in the link to the spec)
51 / 18 / 2
This is the highest rogue dps spec at the moment for single target raid dps.
Talent Options - The only choice here comes with the 2 points at in assassination in fleet footed. You can put these points in fleet footed because run speed cuts the down time when you have to move and are not attacking. You could get quick recovery if it’s an encounter where you’re going to take a lot of damage and need a lot of healing. This spec has its highest damage output with envenom spam, so you don’t need to rupture on a raid encounter, therefore bloodsplatter is not necessary. If you are speccing for 5 mans or 10 mans however, and you don’t have another party / raid member with bleeds, you may need to rupture to refresh hunger for blood occasionally, so it might be worth picking up blood splatter with these 2 points in that scenario. Ultimately it’s not a big choice and fleet footed is generally your best bet.
20 / 51 / 0
This is the highest combat dps spec at the moment. It stacks up fairly well when compared against other classes, but at the same time falls well behind assassination. It may look wierd with 1/3 vile and 4/5 improved, but this spec is the one that comes out as best on spreadsheets.
Talent Options - The only thing that should be changed is the weapon spec, depending on your weapons obviously. You may also consider playing around with the poison talents, but like I said this is mathematically the highest dps spec for combat.