I actually try to play Malphite almost exclusively in the jungle, only popping out to Top lane to counter certain AD tops, like Olaf or Riven.
Magic Pen Red's for harassment with my Q, and some later game scaling
Armor Yellow's for increased durability and damage.....they should always be on Malphite :P
Magic Resist per level Blue's for durability. Your a tank, you have to be able to take some spells.
Armor Quints increase your power and provide further durability in the top lane.
Tl;dr: Lots of defensive runes, and only go top against AD champs. Malphite struggles against AP or Hybrid champs like Akali, since he has to stack Armor to be powerful. By choosing to focus almost entirely on Armor, you can become an immovable monster in lane, with some powerful pokes.
Hope this helps