Pros:

Can farm safely
Pressures lane very well after level 6
Great ganks after level 6
Melts tanks and tanky dps

Cons:

Ultimate easily interupted and attracts enemy focus
Gets harassed easily by AD Range type champions in mid
Hard countered by Quicksilver Sash

I use ap/level blues and yellows because my playstyle with malzahar is very passive. I prefer to farm until lvl 9 or so and obtaining a Catalyst Protector before harassing the lane heavily. However if the opportunity presents itself I will gank lanes that need help post-level 6.

The movement speed runes are amazing on Malzahar because it amplifys the pressure on your lane opponent because if your opponent is slower than you, you can hit for free damage with your E every time.

Standard AP masteries that use Ignite/Flash

Starting with a mana crystal allows you to rush a Catalyst Protector. Catalyst protector gives incredible sustain in lane and allows you to farm and harass without any mana issues. With movement speed runes I usually pickup a catalyst before Boots.

After Rabadon's Deathcap, if the other team has a lot of stuns, knockups or silences that can interupted your ultimate, pick up a Banshee's Veil first before the voidstaff. Rylai's Crystal Scepter is a passable last item that increases survivability and allows you to kite even better.

The reason for leveling Call of the Void first is if there is a possibility for a level 1 team fight. Use it to charge up your passive 3 times at spawn so on your next cast, it will summon the the voidling. At level 1, an AoE silence along with a free minion that fights for you will give you a significant advantage to win the fight.

Max out Malefic Visions next because it is your main form of dps and farming skill. A point in Null Zone at level 4 to compliment your ultimate at level 6.

From level 1 - 6, try to farm only with auto attacks. There are 2 reasons why you do this:
1) To maintain the lane at the center so that you are safe from the jungle
2) Malefic visions does not do enough damage to jump to all the creeps and will eat your mana

Once you get level 4 in Malefic Visions or a catalyst you can star nuking the creep wave with your skills. Use E on range minions and Q the line of range minions. Malefic Vision will jump to the melee minions once the ranged ones are dead. There are 2 reasons as to why you want to nuke the minion wave as soon as you can.
1) Pushes your minion to the opponents tower making them lose out on cs
2) Just as safe as last hitting with auto attacks because if you nuke it fast, assuming you are mid, the creeps with reset back into the middle. You can repeat this over and over again while staying relatively safe.

The skill sequence of Malzahar most optimal burst potential is:
Wait until you have your voidling passive on your next spell cast (More damage)
Q (Silence your target so he cannot flash)
E -> W -> R (This sequence is best done all within half a second)
Ignite -> E -> (With bluebuff, your E will be off cooldown after your ult)
2 Voidlings :D

If you see your opponent has a Quicksilver Sash, DO NOT DO THIS unless they have used their active recently. If you do this, all your damage will go down the drain and for 5 seconds you can only stand there looking like a tard.

A neat trick to pull off with Malzahar: Use E on minions. If your Malefic Vision jumps from a minion to your opponent, quickly drop w and ult. Your opponent will not expect this.

If your voidling is active, play aggressive. Use your E. Most people underestimate how much damage the voidling does. Keep your voidling in range for it to attack your opponenent to push them out of lane and deny them cs.

Very rarely will you be able to use your optimal burst combo but if possible always lay your W under your target before you ult them. Your dps drops significantly if you do not.

Malzahar is a Tank nuker. You can quickly shutdown a tank or tanky dps that is trying to get into the middle of your team to disrupt the carries. Do not hesitate expend your burst on a tank to give your team a smoother teamfight. Only use your ult on the other team's carries if you know you can do it for the full duration or if your target is going to die and you are going to live. Do not trade death for death because Malzahar depends on being able to stay alive to deal his damage since Malefic Visions is a DoT spell.

Sometimes all you need to do is ult to supress for your teammates to catch up to your target

Champions that work well with Malzahar on a team:
Cho'gath (More silence)
Morgana (Blackshield so you cannot be interrupted during ult and MR reduction)
Amumu (Allows your w to hit the other team for up to 2 seconds)
Warwick (With both your ults, its almost a guaranteed kill at level 6 from a gank)

Malzahar is an AP pick that is situational. If the other team is built around tanky dps with gap closers and fast movement, Malzahar is a good pick. For example if the other team has some of the following champions:
Irelia
Master Yi
Xin Zhao
Renekton
Nasus
Usually these type of champions rush straight for your AD carry or YOU in a teamfight and you can shutdown them hard but positioning is important.