If my team already has a high damage AP mid or something I'll go 9/21. If I'm the team's main source of AP damage I go 21/9. Honestly I usually just go 21/9, though. For runes I like mpen, armor, scaling mr, and ms. Build mpen and then tankiness. DFG is okay if you're really snowballing.
You start Elixer 1 Red Ward, or Boots 3 Pot. First item you really want to buy is a Haunting Guise, or Sorc shoes depending on the laner opposite of you. Haunting Guise and Sorc shoes are the two static items you'll have every game.
From here you usually want to build very tanky, depending on the game this is where I build Warmogs, Sunfire, or Abyssal. Elise is a champion who scales very well into the late game while having poor AP ratios, as long as you have high MPen your golden.
Finally for Masteries I go 21/9/0 if I feel confident, or 9/21/0 if I feel like I need the extra defense. Hope this helps!
PSN/LoL IGN: XxShadiusxX Ganking from the forest as the forest