I play Malphite exclusively in the Jungle. These are my experiences.
The best rune's I've used so far are Attack Speed Reds, Armor Yellows, MR/LvL Blues, and Armor Quints. THey help me clear the jungle fast and I have great HP Resilience through the jungle.
When I play Malphite jungle, I either try to gank lanes that are absurdly push into my teammates turrets, hold a lane if someone has to back, or farm my jungle. Normally a game will be me trying to get to 6 as fast as I can, then I gank a lane. I'll build Frozen Heart to give me some mana for extended fights since malphites spells cost a lot of mana and it really helps vs AD Carries, Jax's, or anyone who's attack speed based. I frequently am up against champions who have a ton of attack speed, so Malphite works well against them. Except for Udyr's because they farm their own jungle so fast that they leave me in the dust with levels and items.
I think my biggest successes with Malphite involve either having a team that can syngergize well with my knockup ult, or being against enemies who get destroyed by my attack speed slow, giving my team a huge edge (My Frozen Heart provides 15% attack speed slow, and Malphite himself has a 50% attack speed slow, 65% attack speed slow negates an item's worth of attack speed and then some).
My biggest complaints with Malphite are my slow ability to clear my own jungle, high mana costs. I think if Malphite were better able to clear his own jungle I'd feel a bit more useful when im against .... well any current meta pick jungler really. I actually do pretty good against jax junglers, he kinda seems like a meta-jungler-pick.
Just let me clear my jungle faster. That alone would be amazing.