Well, I play Jax mostly, with a build roughly like

Ninja Tabi
Rageblade
Hextech
Atma's or Banshee, depending on enemy team comp
Other from above
Black Cleaver/Frozen Mallet

So what sort of runes should I be using?

Dodge runes are important for your E stun.

Id imagine. I have full yellow dodge. Should said that.

Other colors is what I'm asking about.

AD runes.

Gives you a little hp at the start.

You are doing half magic and half attack damage anyway so penetration is not really required.

ad + ap runes are nice they give you such a good damage boost + health boost early game

Armor pen marks, dodge seals, flat CDR glyphs. quints can be whatever you think is best.

AD and AP runes are pointless since they dont help jax with his passive, better to help other things such as attack speed

They don't help with his passive? You know his passive is extra hp based on AD and AP don't you?

If you get the flat attack boosts this can be hugely helpful early game not only for the attack but for the extra sustainability from hp. If you start with full AD reds you get an extra 30 HP at beginning plus the equivalent AD of a sword.

I got speed quints personally. With nimbleness plus this you can outrun most people who try to escape.

For blues I got AP per lvl just to fill it out.

For blues I get magic resist because he's quite weak earlier in the game. With Doran Shield and the 13 MR he gets from the blue runes, he becomes that much better in laning phase. Don't let your Jax get harassed out of lane, or he might get gimped throughout the game.

The thing about jax is that he can out harass most opponents (excluding ranged) because of the huge damage of an empower+leapstrike. With a couple of hits of this they will be unable to get close due to low hp.

I'm guessing you use the 0 21 9 mastery tree instead of the 21 9 0 mastery tree so really they're fairly incomparable as far as styles go.