Here's for me, the best build for Malzahar.
Runes, Spells and items just get him OP for 3v3 and 5v5 battles.
The only item who changes sometimes is Mejai. It's an item stack item so buy it if you're sure to get some stacks, If not, you can buy a hextech revolver or a haunting guise to get AP for low gold, very useful in early game.
I chose a great AP and magic penetration stuff and runes, because I think malzahar is one of the best caster of the game, able to do lot of DOT damage and BURST damage. So well played, with lots of damage, you should have fun :)
Anyway, With this build, a good playing, and a good team, you should win everytime, or almost :).