Malzahar is a beast. I would say he is the single greatest AP caster champ in the game. The really neat thing that makes him different is he isn't burst DPS. His silence can burst, but it is a skill shot that you can't always rely on and it will only do upwards of 500-600 damage anyway. The reason his damage over time is great, the bad guy doesn't know he is dead. You can kite the hell out of champs with Malzahar while they slowly die. To this end, I have made a build that I think takes advantage of his unique skills which is a bit different than most people build him. And I always beat any other Malzahar that plays.
In order:
1. Kage's Lucky Pick
Gold items are important for champs that can't farm well, and Malz farms better than anyone. So this means you get gold faster than a pimp deciding what color teeth to get in the grill shop.
2. Sorcerer's Shoes
Don't think I need to explain the importance of magic penetration.
3. Hextech Revolver
Yep, this is my first real item. I build up my AP base while getting that much needed spellvamp. Spellvamp helps with kiting, but it also has saved my ass so many times that I can't imagine not using this item. Your ult turns into a drain that can sustain you in team fights, your silence is burst heal, and your dot just bounces around healing you the entire time you are in lane.
4. Fiendish Codex
The second part to Deathfire Grasp, it gets some mana regen and CDR that will be helpful throughout the game. We don't fully upgrade it just yet though because we want to keep the gold coming for now.
5. Rylai's Crystal Scepter
Health, AP, slow. Every AP caster should get it. Again you live longer, now your spellvamp helps more, and your dot is a constant slow for better kiting.
6. Will of the Ancients
Upgraded Hextech for more AP, more Spellvamp, and gives spellvamp to your teammates. They may not realize what you just gave them, but it will help!
7. Deathfire Grasp
AP, mana regen, CDR. Rounded item good for any caster, but it has a bonus. The active ability hits a champ for 30%(+% based on AP) of their current health. DESTROYS tanks. Drop null void, hit grasp, ult... Your null void does damage based on max health, and should be doing at least 15% by now. They are dead.
8. Abyssal Scepter, Rabadon's Deathcap, Zhonya's Hourglass
This will be entirely dependent on the game. You might even pick something else for whatever you need. AP is always good, but sometimes you need resists against certain matchups.
Ignite/Flash are the only summoner abilities you pick. There is simply no reason to pick anything else. If you are running mid, and you should be, at lvl 6 the other person is dead usually. As long as you are doing good harassing, and you should be, they can't survive your flash/ult combo. Unless they are morde or nidalee which are both your toughest matchups. Your runes should get you CDR and magic pen at the very least.
Don't be mistaken into thinking you should get Void Staff or Archangel Staff. Void Staff is better replaced by Abyssal Scepter and Archangel Staff doesn't really give you anything aside from more mana regen than you need.