Jax is one of the best duelests in League of Legends. He can pretty much 1v2 just about any combo (except if both have silences/stuns). He can stun every auto-attacker DPS unless they activated Sword of the Divine's active. His ult allows him to increase his magic resist scaling with his dodge percentage. This allows him to take on even really strong nukes because with the added MR he has his spell vamp and lifesteal.

For runes i suggest Magic Penetration Marks because with his ultimate you receive a somewhat auto-attack passive that for every third attack his attack deals extra Magic Damage. This means with these runes that makes the damage felt by the enemy is increased. It is MANDATORY to have Dodge seals. This is required because Jax's E ability becomes available every time he dodges an attack. For Glyphs i personally use Magic Resist/Level. These are not as crucial as Seals. You can use flat ability power for extra kick early game, CDR (Cooldown Reduction) to... reduce cooldowns, Ability Power/Level for extra Ap late game but these really aren't as useful as one might think. Personally i believe the Mag Resist glyphs are the best choice. And for Quints i use Dodge, and once again these are mandatory.