While Flat CDR Quints and Glyphs were quite popular last season, that was largely because they would allow you to get 20% CDR at level 1 (letting you cap with either Frozen Heart or a combination of Glacial Shroud and Kindlegem). That build is less useful in Season 6 due to losing 5% CDR from Masteries and Trinity Force and Iceborn Gauntlet getting +10% CDR.
I would recommend using Armor Pen Marks over AD Marks if you have them. Nasus players typically freeze the minion wave near their tower, so you will have plenty of experience last-hitting under tower. Armor Pen scales significantly better on Nasus since it will increase the damage dealt by his Sheen and Siphoning Strike and it will scale better with the AD from his ultimate and Armor Reduction from E.
Also, I would recommend using Lifesteal Quints. They provide a significant amount of additional sustain early- and late-game, letting you survive longer in fights and when farming.
I would recommend taking either Thunderlord's Decree (early poke) or Grasp of the Undying (for sustain and short trades) on Nasus, though I will probably have to try out Fervor of Battle and Warlord's Decree on him at some point.
While 5% CDR from intelligence may be nice, Precision will significantly increase the damage dealt by your Q and ultimate against squishy targets. Nasus scales incredibly well with flat penetration but he has trouble itemizing it, so take what you can get. You may stack slightly slower, but you can Q every minion in a wave at 40% CDR anyways.
General item order on Nasus looks something like the following:
Vs. AD:
->
->
->
->
Vs. AP:
->
->
->
-> 
Obviously, you can adjust your build as necessary, but that is a nice starting point.