Mobafire's system doesn't properly account for the statistics on this build. The percentage bonuses throw it off, and it doesn't add in masteries. These are the corrections, and some unlisted numbers I think are important.

Mana: 2749.79
AP: 540.93
Magic Penetration: 83.09 + 0.15 of target's MR
Cooldown Reduction: 24%
g/s: 2 g/s = 120 g/m = 3600 g/30 min (up from a base of 1.4 g/s = 84 g/m = 2520 g/30 min)
Exp Gain Boost: 5%

This is my first build guide. Malzahar was the second champion I ever played and the first one I really feel I mastered.

The over arching program of the build was suggested to me by my roommate and friend, who used a variation of the build described in "You've got something on your face" so all respect there. This is just my spin on things, mostly for my personal use.

The strategy is to get magic penetration up very quickly, thus eliminating much of your opponent's defense (in order to block any of your damage, they have to have a Magic Resistance >83.09) Clearly, it is unlikely that any champion will block a substantial portion of your damage, as the base magic resistance of most champions is 30. The 15 percent from your mastery scales, so you're guaranteed to do a bit either way.

Once your magic penetration is up, you can focus as much as you want on AP. I usually have all my penetration done after the first 15-20min. Most of your AP items are already there, you just have to get Deathcap and Deathfire Grasp. Make sure you get Deathfire last! It uses Kage's Pick, which is what makes getting everything else quickly possible.

The runes were chosen for reasons that are apparent given what I just described as the strategy for this build. Don't forget that the seals also add AP because of Archangel's. To be precise, they add 5.68 AP. Switching any of these runes for AP, Mana, or more penetration wouldn't be too harmful.

Some of these points are simply there to get your further. Some changes that would be reasonable:

Exchange Cripple for Plentiful Bounty.
Exchange Spatial Accuracy for Haste.
Exchange Insight for Anything in utility, maybe Good Hands.
Switch from ignite to get Presence of the Master.

Most of these are based on what summoner spell's you prefer.

Dorian's Ring is there because I like to mid, and that ring give's you the edge (unless, of course, they have it also...) You can get rid of it for maybe the Tome, which builds into Kage's Pick, or for the Boots of Speed. If I'm not midding, I go for Kage's right away.

The one real downside of this build is defense. I haven't done much to compensate for Malzahar's squishiness. If you would like more survivability, I would exchange the Death Cap for Zhonya's Hourglass. Also, when playing against other mages especially, Banshee's Veil isn't a bad idea. I would throw away Deathgrasp for it.

The only real reason Deathgrasp is here is because Kage's Pick turns into it, so you save money. You can replace it with Rylai's Scepter, or Will of the Ancients. Don't bother with Abyssal Scepter though, you don't need the Magic Resistance lowering aura. Moreover, you don't really want to be too close anyway.

The only other thing is that I think you should get Kage's as soon as you can (after the ring). The sooner you get it, the better your return on investment.

I'm going to list exactly what each skill does in damage with this build.

Minion: The voidling adds some DPS to Malefic visions.
Call of the Void: 732.74 magic damage, silences for 3s (6.84s cooldown)
Null Zone: 52% of MAX health in magic damage(13% four times, once each second)(10.64s cooldown)
Malefic Visions: 752.4 over 4 seconds in magic damage. Recasts on a close enemy if original target dies before the 4 seconds. (5.32s cooldown)
Nether Grasp: 1253 magic damage over 2.5s. (60.8s cooldown)

I get malefic visions first. I do this because it has the lowest cost. You just have to be careful.

If it kills, it gives you back 10 mana. The spell costs 60 at level 1, so if you can kill 3 minions that it get's on it will only cost you 30 (it gives you 10 mana each death). This makes you much more able to sustain a high DPS output early game than you would with Call of the Void. Since you are killing minions faster, you level faster. I tend to be three to four levels ahead of my team midgame. just be sure to cast it on week minions first, and ones that the other minions are hitting. Careful selection will reward you, especially if you have your voidling.

I like to focus on clearing minions. So the next skill I get is Null Zone. Early game, minions make a big difference, collectively they put out substantial damage. If your opponent doesn't have any to support him, he'll run or you'll kill him. Either level's you more quickly.

I usually put one point in Call to the Void (It's primary purpose is for the silence) before level five, when you get your ult. At this point, you won't have enough DPS to kill a single champion on your own, wait till they wonder into the tower. When they stop to hit you, Call to the void, Malefic Visions, Null Zone, and then Nether Grasp. The order is important to maximize damage. Make sure to put null zone a little bit behind them so they don't run off of it while you are casting nether grasp.

I use ignite and either Flash or Teleport. The reasons are should be fairly apparent: Ignite for the last hit you might be missing, and Flash for running or for setting a trap. Teleport can be nice to get you around the battlefield quickly, giving you more kills.

That's all I've got. Sorry the page isn't very fancy. Malz is a lot of fun, especially when you quatra kill four champions with one Malefic visions >=)