As a mage I've had my fair share of rogue problems. I've tried alot of builds, but the one I'm now (deep fire) handles rogues better than the rest, if you consider the cloak of shadows. My earlier PoM spec (hadn't got AP because IMO it sucks, just wastes your mana) was mostly about luck, but the arcane missiles worked pretty well, and a instapyro (for the dot) held them out of stealth.
Later on (60-67) I went frost and with this build rogues who hadn't got Imp. Sprint was pretty easy, but those with it was hard to beat. Frost nova and frostbolts, ice lance when I got it, and some use of the elemental's freeze (really a good thing to have) could usually bring em down to 20% when they most of the time vanished. If my nova was on CD then I couldn't do ****.
Now I'm deep fire and my instants can take care of them pretty good - but now they have the damn cloak. Now it's more of a dice throw, if I get to blast them away they haven't got a chance, but usually they open with garotte silence. Nova-lance, fireblast, breath, blast wave, just get the damn instants off. Try to keep them controlled, pray that you get an impact or even two. Should get them down, if they cloak it's just good for me. I hold a little, kite and wait for my CDs to shorten. Only problem is I haven't got any survivability-improvers like ice block or pom-sheep.
I am not very good at PvP but this is what I try to do atleast^^