Catalyst/RoA. It lets him sustain his harass forever in lane, and he can use the AP.
Cooldown reduction, AP, more Damage, and faster gold: Get Kage's and Codex, and when you want, turn them into DFG. Morello's is an alternative here, but DFG is very nice as Zilean only has two sources of damage otherwise -- Q, and autoattacks.
More CDR! Tanky Zil's get Frozen Heart.
Shoes: Daring Zils get Sorcerer's Shoes. Some might get Speed 3 boots, but Mercury's Treads are better. Lucidity boots aren't awful if you're having trouble itemizing for CDR.
If you're playing him more Supportive, CDR takes high priority over AP. If you're playing him offensive, which is harder and less rewarding in my opinion, build massive AP. Early mana is very important, and tankiness never hurts -- although he is NOT a tank.