I'll detail some ideas for AP rune sets below.
For Marks, Magic Penetration runes are by far the best choice as spell pen is harder to itemize in-game than AP. Less so in season 3 since the new items but still, the early game damage increase is very significant. Most AP casters will also rune up Magic Resist blues so the spell pen runes are almost a necessity to counter your lane opponent's MR.
For Seals, there are basically 3 choices; Scaling AP, Mana Regen (flat or scaling) or flat Armor. Scaling AP seals are well suited to burst casters with huge nukes such as Annie or LeBlanc and even work well for DPS mages like Karthus or Cassiopeia. Mana Regen runes are a niche pick for champions with early mana problems like Orianna. Flat armor seals are useful in two situations; the first is when you are unfortunate enough to run into a Talon or Lee Sin mid. The other is when you are playing an AP top lane against a bruiser like Darius or Pantheon. Flat health seals are 4th option but I would only recommend these for one mage; Vladimir.
If you are playing an AP mid, I would almost always recommend taking MR blues (flat or scaling). Flat MR blues are better against mages with a lot of early game damage (Annie, LeBlanc, Cassiopeia, Sion). These champions are geared towards getting fed early game through kills rather than farming their way to victory (like Morgana or Karthus). These runes will help you deny them those early kills by making you slightly more durable. AP/level glyphs are also fine if you know that your opponent does not have a lot of harass. For example, if you're playing Swain against Nasus top, you're not so worried about taking damage as much as not allowing Nasus to farm. AP/level glyphs would be fine in this case.
Finally, for quintessences, there are really only 2 main choices; movement speed and flat AP. Flat AP is a safe bet for mages who have a built-in gap closer (LeBlanc, Akali, Ahri, Katarina, Kassadin etc.). Movement speed is essential on melee mages (like Cho'Gath or Sion) or champions with inherently low movement speed like Ryze. Ryze is also terrible at pushing lanes so roaming comes with the job. Flat HP quints are also very good but again I would only recommend them for Vladimir as they are exclusively geared towards early game survivability and the +80 odd health does very little late game.