Shen is very versatile when it comes to runes. I personally run 9/21/0 on Shen taking the flat AD and CDR. I take a flat AD Quint and two Attack speed Quints to compensate for my lack of AS. I then take flat AD for easier time last hitting and trading in small fights, Armour Seals, some MR per level glyphs, and some flat CDR glyphs. With the CDR runes, I can run 10% CDR at lvl 1 which is great for lower cooldowns on early game ults. I'm all about trying to get as many Stand United out as possible. Or you could totally swap out the CDR for MR when playing ranked and if they are playing an AP top laner.
Realistically, you can run basically a large variety of runes on Shen and the one suggested by DXHaseoXD is great as well, leaning more towards the defensive side.
I tend to go more aggressive going for level 2-4 first bloods with the Ignite and raw AD. It is honestly all on your play style of Shen and what works best for you. Some people like hybrid-pen, some people like, attack speed marks, etc etc.
For more information, check out my guide for more info: http://www.mobafire.com/league-of-legends/build/yummy-rices-guide-to-top-lane-shen-the-flippin-ninja-395771
From Yummy Rice, devoted
pai player