Ah, rogues. These are the guys that ganked you back in STV when you were leveling. Now you're 70 and ready for some revenge, right?
Rogue fights are some of the more interesting matchups in my eyes. It basically becomes a cooldown war, where the mage starts off playing defensively to burn the rogue's cooldowns, then switches to a more offensive mode to finish him off. A rogue with no cooldowns is a sitting duck, and learning how to avoid specific cooldowns will greatly help you achieve victory.
Most rogue specs play similarly, though there are a few important differences that will be noted below. For example, a Shadowstep rogue (not that there are many out there) may scare you with an enormously damaging opener, but as long as you keep them out of stealth after that they should be cake to fight since they really have very little damage output besides their vicious opening ambush. Take a look at the rogue talent trees sometime and play around with various combinations to see what limitations you can find like this!
Please note that the information below pertains to a frost spec mage, as that is what I have confidence in playing myself. Some of these strategies are universal to all mages, but some may have to be tweaked if you decided to go heavier into fire or arcane.
If you're interested in more information and more advanced strategies against a rogue, check out Radikal's (incomplete) dueling guide here.
Openers
The following are abilities that the rogue will use from stealth to open up on you.
Sap
This simply incapacitates you and does not bring the rogue out of stealth. Most rogues use it to simply keep you from running around and spamming AE at them. With talents (Dirty Tricks, second tier of Subtlety), the range of this move makes it possible for the rogue to sap you without fear of AE. Even without it, a good rogue can sneak in between AE pulses and get you with it.
If you find yourself Sapped, the only way out is either a trinket or an ice block. 99% of the time you'll just want to sit there and take the opener anyway, but if you're feeling lucky you can attempt to trinket and immediately nova to catch them off guard. Usually not a good idea, but it'll annoy your friends in duels if you can pull it off.
Cheap Shot
Generally this is not a smart move to use against a mage. If you are Cheap Shotted, Blink immediately but do beware of a followup Kidney Shot, as you won't be able to Blink out of that. Some rogues also have talents to make you take significantly more damage while Kidney Shotted, so beware of this. Still, just make sure to keep range after the blink and generally you'll be all right, since if you do it fast enough they generally won't be able to have time to snare you anyway.
Ambush
The only time a rogue will ambush you (besides the bad ones) is if they're Shadowstep. If you find yourself the victim of an enormous Ambush opener, rejoice! While it may be scary, this is the most damage the rogue will really do to you, and if this occurs your #1 priority for this fight is keeping the rogue from restealthing to do it to you again. A rogue using a big Ambush is also a sign that the rogue has Preparation, so be prepared for a double Vanish.
Garrote
This is what you'll get hit with by most of the good rogues. It deals a decent amount of damage, but more importantly silences you for 3 seconds. If you're hit with Garrote, immediately try to simply run away, preferably towards the rogue. While this may be counter-intuitive, if you manage to run through the rogue before he uses Shiv, you may be able to escape unsnared. If nothing else, it'll at least escape an autoattack or two or disorient the rogue. Make the rogue work for his damage while he's got you silenced. This may be followed with more silencing effects (such as a combat rogue's silencing kick), though generally you're good to go as soon as it wears off. Generally you should frost nova as soon as you can to make him burn one of his big cooldowns.
A small thing to note, remember that if he tries to Blind you while Garrote is still ticking, the Garrote will cancel the Blind! It's rare this will happen, but even good rogues can get forgetful and not realize they've put this DoT on you when they go to Blind.
Also remember that the rogue must be behind you to pull this ability off. If a rogue is in front of you when he Vanishes, don't turn away and run! Strafe away instead to keep him from getting behind you and force him to Cheap Shot instead, which is FAR less threatening.
The Small Stuff
The following are abilities you can expect to be used in just about every fight with a rogue, or at least will be available to him.
Shiv
This move will let the rogue do a small amount of damage and (more importantly) apply the poison of his off hand to you guaranteed. Nearly all rogues will use this to put Crippling Poison on you. There is no cooldown, so generally when a rogue gets on you you will be snared if you're not already. There's not much you can do against this besides try to keep distance while unsnared as much as possible.
Kick
Cooldown: 10 seconds
This interrupts a cast and locks out the school it's from for 5 seconds. Generally, casting anything while a rogue is hitting you is suicide anyway, so this really shouldn't even be used much against you successfully. Only cast when you have distance, and even then only if you really need to.
A rogue specced in Combat will probably have a 2 second silence associated with Kick whether he interrupted a cast or not, which can be a bit nasty if he chains it with his opener to keep you "silence locked" while dishing out some nasty damage. Keep this in mind for when a combat rogue gets close to you.
Deadly Throw
A forum favorite, Deadly Throw is a ranged 50% snare that does nasty damage. It has no cooldown, but it IS a finishing move, which means the rogue must have combo points on you to use it. A Cone of Cold with Permafrost will slow the rogue down more than Deadly Throw snares you, so keep that in mind if you get DT'd while on the run and the rogue starts getting close.
If the rogue is wearing his PvP gloves (and you really should assume he is, as most PvP rogues will have these), Deadly Throw can also interrupt any spell being cast and lock out that school for 3 seconds. If you see a thrown item flying towards you while you're in the middle of a cast, immediately sidestep to avoid the interruption and start recasting if necessary.
While the ability does take combo points, most rogues will have a talent called Ruthlessness in the Assassination tree, allowing their finishing moves (such as Deadly Throw) to have a 60% chance to add a combo point when used, leaving them with a lone combo point after the first DT that will let them DT again, which may let them DT again if they get Ruthlessness a second time. This may chain on for quite some time, so don't count on the rogue having no combo points after the first (or subsequent) throw.
The Big Stuff
The following are long cooldowns that will be available once per fight (some twice if they use Preparation). You should generally assume a rogue can and will use all of these abilities in any fight, though in BGs it's more likely he'll only use a few (if any) due to the cooldown length.
Vanish
Cooldown: 5 minutes
This famous cooldown will make the rogue vanish, putting them into an improved stealth mode. The cooldown becomes 3.5 minutes with Elusiveness, a popular talent in the Subtlety tree, but either way it's only going to happen once per fight unless the rogue uses Preparation.
Vanish also removes all snares and roots. Usually a rogue will use this after you frost nova them for this reason, though they may also use it if they're simply snared and far away from you.
It's also very worth noting that any spell that is in the air will generally not hit the rogue if he vanishes before it hits him. Vanish is slightly buggy, however, so if you get lucky the spell in the air may hit anyway, knocking them right back out of stealth! If a rogue is standing in your nova and he has not blown Vanish yet, be prepared for him to use it as you're casting or when the cast just completes.
There are a few excellent counters to this move. Any damage taken immediately after the vanish will pull the rogue back out of stealth. If you are far away from the rogue and you think he may vanish, prepare a rank 1 blizzard and center it over where the rogue is. The moment he vanishes, blizzard to uncover him again. If the rogue is close to you, use Cone of Cold to uncover (and snare) him. You should generally save Cone of Cold until the vanish for this reason if possible, since it has longer range than an Arcane Explosion (your last resort), does more damage, and has the snare effect built right in to keep the rogue at bay. Also note you can use your water elemental's freeze ability like Blizzard, but with the added bonus of re-rooting the rogue if it hits. On the downside, you'll have your WE freeze on cooldown if you miss, but if you're quick it's an excellent way to bring a rogue back out. Practice a bit with this method when you can.
The real key to countering Vanish is predicting when it will occur. Even a fraction of a second of delay can let the rogue slip away from your AoE effect, which means he'll get another nasty opener on you. If the rogue does manage to get away and you don't know where he is, immediately start running away from where you last saw him to let your shorter cooldowns reset, and bandage if possible.
Global Cooldown Management, as mentioned in I Suck At PvP, is very important in swiftly countering Vanish. If the rogue hasn't blown Vanish yet, but you suspect he's about to, wait a moment before casting anything to see if he does. If you try to ice lance a rogue that's been nova'd, and he vanishes out of it, you have to wait a second and a half before you can CoC. This second and a half is ample time for the rogue to either get another opener or slip away to safety. Instead, wait on the ice lance to see if he vanishes, then cast it to punish him for not if he doesn't or immediately Cone of Cold if he did to bring him back out before he can do anything.
Sprint
Cooldown: 5 minutes
Duration: 15 seconds
This move increases the rogue's speed by 70%. If the rogue is Combat (which you can generally tell by the rogue wielding weapons that aren't daggers, usually fist weapons or maces), this will also break any existing snare or root. Against a combat rogue, you want to try and save your frost nova for after Sprint whenever possible, or at least try to save a water elemental freeze for this one to stop them in their tracks. Remember, it'll break an existing snare or root, but doesn't stop new ones from being applied at all.
A rogue moving at 170% speed can still be stopped with a Cone of Cold, especially with a permafrosted one. Cutting the rogue's speed in half will put them down to 85% (68% with permafrost), still slower than normal running speed. Of course, this assumes that you aren't snared yourself, which against a good rogue is often unattainable. Still, if you find yourself unsnared this is a good thing to keep in mind to get him away or otherwise buy yourself a few more seconds.
Sprint is often coupled with Cloak of Shadows, and I'll get into that in a moment. In fact...
Cloak of Shadows
Cooldown: 1 minute
Duration: 4 seconds
Affectionately (or otherwise) nicknamed "Cloak of Skill", this makes the rogue wipe off all magical debuffs and makes him 90% resistant to all spells for the duration. The resist rate is essentially an immunity, and while you may occasionally land a spell (it was a running joke between myself and a rogue friend for a bit), absolutely do not count on it.
As a quick note, if nothing else do spam ice lance on a CloS'd rogue until it wears off. If you don't, the rogue may go out of combat due to not being hit or using any abilities, allowing him to restealth and putting you in trouble. Ice Lance will generally do zero damage for the duration, but it'll be sure to keep the rogue in combat whether it resists or not so he can't pull anything tricky off on you, and it won't cost much mana anyway.
How you deal with this depends on what else is going on and what cooldowns you have available. If you feel you can ride out the 4 seconds of near immunity, it's generally a good idea to do so in order to save your arsenal for later. The only time this really isn't an option is when you're up against a Combat spec rogue with Adrenaline Rush going, because he will rip you up in those 4 seconds if he stays on you. You can attempt to Blink, especially if the rogue just used a finishing move (therefore making Kidney Shot a difficult proposition), which would give you breathing room to wait out the cooldown, allowing you to nova him by the time he gets to you again. The downside is that if he DOES reach you, you're going to most likely be Kidney Shotted with no way out besides trinket or ice block.
You can also simply ice block right on the spot, which is generally a good idea if the rogue is using Sprint as well (since he'd catch you in a heartbeat if you blinked). Just make sure he doesn't run off and restealth, so be ready to cancel your ice block and ice lance or CoC him out of a vanish. If possible, try to cancel the ice block a bit early anyway to catch the rogue off guard so he can't Shiv a crippling poison proc onto you.
Blind
Cooldown: 3 minutes
Range: 10 yards
This will disorient you for 10 seconds, breaking on damage. With the same talent that reduces Vanish's cooldown, Blind becomes a nasty little 1.5 minute cooldown. With Dirty Tricks, the range becomes 14 yards. Still, this is generally a once per fight ordeal. You can use your PvP trinket to escape this or Ice Block, though generally it's better to save your trinket for Blind and Ice Block for an "oh crap" moment (such as CloS + Sprint or Adrenaline Rush) due to the immunity associated with it.