What runes go well with Ahri?

Just don't buy the 9 Greater Mark of Hybrid Penetration.

It may be good, but if you're looking for runes, I'd advise you to buy runes which are great for a LOT of champions. Hybrid pen runes are only good for 2 or 3 champs. magic Penetration runes are much better for almost every other carry AP, and are not bad at all on Ahri.

That setup is fine, in all honesty runes don't make that much of a difference in a match. Personally I run 2x Movement Speed Quints and 1x HP Quint, for the most part runes, masteries, and summoner spells are preferences.

If you plan on playing mid a lot it's always a good idea to invest on an MR page (although not really needed) for the more difficult match-ups like Veigar or LeBlanc.

Rune setup guidelines for AP carries, as of patch 3.8:

• Marks : Magic Penetration. Period. Most of them do not deal enough physical damage to make Hybrid Penetration efficient.

• Seals : Armor or Scaling Health, depending on your lane opponent. Scaling Ability Power seals are NOT primary, thus less efficient. Even as an AP carry, you WILL benefit from defensive seals more than offensive ones.

• Glyphs : Magic Resist, Scaling Magic Resist or Scaling Ability Power.

  If your lane opponent is an AP carry like you, go for Magic Resist.

  If your lane opponent mostly deals physical damage, or if you do not fear his magical damage, go for Scaling Magic Resist.

  If your lane opponent mostly deals physical damage, and NOBODY deals significant magical damage in the enemy team, go for Scaling Ability Power, stack armor and swim in their tears.

• Quints : Ability Power. Even if Ahri has meh ratios, it will help you farm with your spells and improve your early game potential slightly. A few AP carries might benefit more from Movement Speed, such as Ryze ; but Ahri doesn't.