Abilities like Alpha Strike (Master Yi's Q) allow you to disappear for a second and then do damage. This is useful to dodge stuns and skill shots.

Master Yi's W (Meditate) is good when you are running away from a successful dive and are tanking the tower.

It gives damage reduction and heals you based on your current health. It is also good in early jungle fights.

Master Yi's E (Wuju Style) simply does no damage to the cost of no mana. It should be used in the Jungle against mainly raptors in early game.

Now we get on to the last ability Master Yi's R also known as his ultimate Highlander. This ability gives attack speed and movement speed and he becomes immune to all slows and cripples. This ult should be used in team fights, chases, dives, kites and doing solo baron because if you become fed as Yi you can get all your items and start to do baron without your team.

The runes I have used are optimal for Yi because Conqueror is a well-rounded primary rune for Yi. Bloodline is taken because with Yi you are usually going to buy a lot of attack speed but not as much life steal, this is good for doing baron and drakes solo.
Ravenous Hunter is perfect for Yi. The reason for this is that at level 13 with 5 stacks of Ravenous, you can solo baron with your ult, Bloodrazor and Guinsoo's Rageblade. Sudden Impact is also taken because Yi builds a lot of burst usually.