Although Zilean is a support you want to beef him up as much as possible with your Runes. Going mostly Ability Power with a little Magic Penetration is more beneficial than Cooldown Reduction or Mana Regen.

The power of this build comes from the Philosopher's Stones. Since Zilean is a support class and Time Bomb is his only real damage ability, early game you will just be harassing the enemy players with Time Bombs. Try to focus players with Time Bombs and use your mana for only that early on. Don't worry about last hitting minions, you will gain most of your money from the Philosopher's Stones. Keep in mind you can bomb minions who have low hp and hit close by enemies.

As soon as you have enough gold to buy a Philosopher's Stone you want to buy as soon as possible. Start off building for 2 Stones, then pick up your boots. I usually go with the cooldown reduction but magic pen can also be good if you are aggressive with your bombs. Once you have your 5th Philosopher's Stone save until about 5500-6000 gold. You should have your 5th Stone by about 22-23 minutes into the game. Begin replacing your Philosopher's Stones one by one, selling and replacing with the next completed item.

Max your Time Bomb as soon as possible. This is Zilean's bread and butter for doing any damage. Keep in mind Zilean is a support class, but with cooldown reduction and Rewind, Time Bombs can become very powerful.

I usually go with Ghost and Ignite for Summoner Spells. Zilean does have Time Warp for speeding up allies and slowing down enemies but Ghost does stack with Time Warp and can save your life if Time Warp is on cooldown.