Before you accept these scrubs ideas of Ryze masteries, I have Zombie Ryze.
Go either 9/21/0 or 0/21/9. Choose between dmg and ms, I personally go dmg. Contrary to these derps thinking of stacking ms is a good thing, Ms has diminishing returns. Go here: http://leagueoflegends.wikia.com/wiki/Movement_speed
Tl dr, You get Dr at BOTH 415 ms and even more at 490.
You take every single defensive mastery and skip anything else in defense. You also take full out tank runes, no health, just defensives either per lvl or flat. I personally go flat because his early game is horrid, but per lvl would make you a monster late game. Rush Catalyst, ofc getting boots lvl 1. Finish Ninja tabi, then RoA. Depending on how well you're doing and what's going on in the game affects your next item choice.
Are you raping? Another RoA(they stack, ohsnap), Rylais ,or even deathcap may be in order.
These are the items Ryze can easily buy, and do amazing with that you should choose from, depending on your needs:
Banshees Veil, RoA, Deathcap, Ninja Tabi, merc treads, Frozen Heart, Void staff, Will of the ancients, Lich Bane, Hextech Gunblade(if you get lich bane).