AP Malphite mid is one of my favorite things to play in this game. To be honest I thought he would be unplayable after the removal of DFG but honestly it just made him a more healthy champion. Previously, once AP Malph had DFG he could one shot anyone that wasn't a tank provided that he went even or ahead in lane. With the addition of Luden's Echo, AP Malphite still has some one shot pressure on ADCs and APCs if they build no magic resist which is oh so satisfying.

Runes are pretty basic. If you're playing draft or ranked you could go scaling AP blues against AD champs or Health yellows against AP champs but it's not a huge difference.

AP Malphite's masteries want to do as much damage as possible. Your auto attacks don't mean much so no point in picking up things like the weaving masteries and arcane blade. I pick up butcher and feast because AP Malphite is seriously awful at CS.

The most important item you can get with AP Malphite is Luden's Echo. On top of having the 120 AP and the burst from Luden's passive, you also get movement speed which helps position you for ultimates. I'd say Zhonya's is pretty important to get at some point even if you aren't facing an AD mid because if you have to initate a fight you want to hit all your damage buttons (R-E-Q) and then be able to Zhonya's so the enemy team doesn't blow you up after. Void staff and Abyssal are huge items because with a little bit of penetration, you can one shot most ADCs if they haven't built any MR yet.

Basically you level R whenever you can for obvious reasons, you max Q first for harass, E second for damage after your ult, I don't even put a point into W early on because it's a waste of mana and the passive on it can sometimes make you miss CS. Whenever you do level W the main use for it is to pop it before you ult so your E can do a little more damage.