Since I already wrote 4 builds, there are not very much champs I'm realy pro with. But omg this brainy called Heimerdinger, I just couldn't skip him.

Greater Mark of Magic Penetration is just for magic penatration.
All those seals, they are only for one thing, MANA .
Greater Glyph of Scaling Ability Power gives some nice AP @ lvl 18.
Greater Quintessence of Ability Power gives much early AP to pwn your opponent with.

Another great choise is Greater Quintessence of Movement Speed but, I like the Swiftness masterie more.

Take 21/0/9
Pick just the normal AP mastieries in offense.
Get Expanded Mind for more mana, get Swiftness because your low movement, Runic Affinity for the blue's you get, and Summoner's Insight for flash.

This chapter has difference between the two Heimerdinger builds.

Personal I don't realy care about the mana hungryness of heimer. So I just go for AP carrry. Open with Doran's Ring it gives you some nice damage and health, pick Boots and Amplifying Tome when going back. Rush Sorcerer's Shoes, because you just need the Movement Speed. Get Rylai's Crystal Scepter, it gives you defensive powers, and your turrets will slow without your ult. Get Hextech Revolver, your turrets will shoot your life back, how nice is that. Add Rabadon's Deathcap for nice burst. Zhonya's Hourglass, gives some nice armor, and you can get yourself save when your turrets are stilll shooting. Get Will of the Ancients its just to upgrade your hextech. Sell your doran's for another Rabadon's Deathcap and your build is finished.

Do you like to spam? Then you will need mana, so get it.

Open with Meki Pendant and some potions, rush tear of the godess it gives you a nice amount of mana. Get sorcerer shoes for the movement speed. Now get a kage's lucky pick you need some AP, and you can sell this item, because at late game it gave you some much gold. Get archange staff it gives great AP and mana. Chalice of Harmony gives some more defense, and some nice mana regen. Then pick Rod of Ages, some nice health, mana and AP. Glacial Shroud gives nice armor, and some CDR that helps you to spam. Athene's Unholy Grail is just a great item for mana, just get it. Pick Frozen Heart as upgrade of your glacial shroud. Now sell your kage lucky pick, it gave you enough gold, for a Rabadon's Deathcap.

If you are the AP carry, max H-28G Evolution Turret first, it's your damage output. The rest of your abilities aren't realy important.

But are you the mana heimer?, then upgrade Hextech Micro-Rockets and Ch-1 concussion grenade fast, these spells are to spam your opponenent.

As with all ultimates, max UPGRADE!!! whenever you can.

Flash, heimerdinger has no escape things, you will need this to escape.
Ignite, with AP carry it gives some nice extra damage.
Clarity, is a mana spell, pick it when you want mana.

other nice ones
Exhaust, is some nice extra CC.
Teleport, can keep you in lane.

Farming is extreme easy with Heimerdinger, if you have enough mana, use your grenade and rockets, but your turrets can also help you farming. Are you going back? place 2 turrets, they will keep farming for you, even when you are back.

Heimerdinger needs to play good in a teamfight for a nice result. You need to know where the teamfight will be, and get turrets there. If the teamfight starts, get away, pop your ult, and throw your other abilities, you wont die, but your turrets make a PENTA for you.

Heimerdinger counters

These short-ranged can only get to your turrets, they wont get you and you can easy win of them

Heimerdinger get countered by

All those assassins they get close to you, and will easy kill you.