All of you players looking to make the most of Master Yi... welcome! I'm Esaelon, a currently unranked player but one who sometimes overthinks things and has a strong math background. Based on my dissatisfaction with many builds which too often resulted in champions getting marginalized or having less damage output than their potential, I've crafted my own custom build, which you see here. I'll explain why the build is how it is, and a few ideas on how best to use him. This is my second attempt at a guide, so please rate and comment, and most of all... Enjoy! (INCOMPLETE as of 2013-04-1: not joking!)

Pros:
One of the few champions who blends burst and sustain (Highlander)!
Good chase using Highlander (immunity to slow) and Alpha Strike (dash)
Flexible: can be built AD/Crit or AP

Cons:
Squishy (Life steal helps AD, Meditate helps AP)
Melee, countered with hard CC (snares, stuns, etc.) (regardless of build)
AD build countered with Thornmail; AP build countered with tankiness/MR
Once ultimate is on cooldown, can be virtually harmless
Ultimate uses tremendous amounts of mana (Especially AP but AD also)

AD build: Armor penetration marks, life steal quints, flat armor seals, scaling MR glyphs.
AP build: Magic penetration marks and quints, scaling HP seals, scaling AP glyphs.

Experimentation suggests that there are viable alternatives. More later!

AD: R>E>Q>W, with Q(1) at 1 and W(1) at 4. Get E(3) by 5, max at 9.
AP: R>Q>W>E, with E(1) at 4. Get Q(3) by 5, max at 9.

AD: Armor penetration increases your damage output significantly, especially as you gain ranks of Wuju Style and before you finish building Last Whisper, and cannot be underestimated. Having 6% Life Steal from quintessences will turn the massive damage you do with your AA into surprisingly enough extra survivability.

AP: Magic penetration increases your damage output significantly, while CDR is your bread and butter: do not neglect it, and get Crest of the Ancient Golem as often as possible. You have one of the best harasses of the game, USE IT.