Zilean is not a support. He's a support mage, so build him like a mage.
Runes: mrpen marks, because they're the only decent mage marks.
seals are probably best as mana regen, but armor could work too.
glyphs and quints should be AP, so your laning is super strong.
Masteries: 9/0/21 is best, because there's not much other options for mages. All the masteries here should be common sense.
Summoners: Flash/Ignite, because flash is amazing and ignite secures you those kills when you bomb + ignite.
Items: Start Boots
and 3 Health Potion
s, because that way you...