Runes, as well as items like Sorcerer's Shoes and Haunting Guise offer FLAT penetration (i.e., you ignore up to X) of your opponent's MR.
The "average" champion has a base MR of 30, that doesn't increase with levels. With ~9 MR penetration from runes, sorcerer's shoes are enough to bring that down to basically zero.
The other options are reduction (triggered by champion abilities like Amumu, Ryze, or Fiddlesticks, or the Abyssal Scepter) which actually decrease your opponent's MR (and so stacks with penetration) and % based (the talent and the void staff). Of these, Reduction is the only way one can bring your target's MR below zero.
When a single character benefits from one or more of these, they are applied in this order:
- Flat Armor/MR Reduction
- % Based Armor/MR Reduction
- % Based Armor/MR Penetration
- Flat Armor/MR Penetration
Some of the above information can also be found in the game mechanics thread on the official LoL forums, here: http://www.leagueoflegends.com/board/showthread.php?t=3287
The answer to your question would then become:
54.36 MR * .85 = 46.206 MR - 8.55 = 37.656 effective MR. (I don't know the formula off hand to convert that to % damage reduced)
LoL has some inconsistent wordings, I'll agree.
I have no hard numbers but I will explain the reasoning for the choices.
My recommendation: Flat attack speed runes in every slot.
The reasoning. His passive scales perfectly with AS and most Warwick builds are based around on hit effects. (Wits end, his passive, Bloodrazor). AS helps him clear camps faster, gives him more sustain and scales extremely well late game.
Armour pen runes - These are a no go in my opinion. 10 Armour pen is enough for jungle creeps to have 0 armour, however Warwick doesn't scale very well with these runes. They may be good for optimal jungle clearing time, however I wouldn't recommend them due to their usefulness falling off pretty hard late game.
Attack damage runes - Warwick doesn't scale so well with AD, so as above, I would not recommend them.
Flat armour seals - I would recommend these on every jungler, except for Warwick. He has build in sustain. You will want to build a wiggles anyway, so the cloth armour will be more than enough for you.
Magic pen runes - These are very strong for lanewick and scale well late game. However, they are not optimal for faster jungle clearing times.
Magic resistance glyphs - These are an option instead of attack speed glyphs. This decision makes your clear time slower. Warwick tend to end up with a fair amount of magic resist through most builds anyway, so I'd say AS runes are preferable unless you are against an extremely AP heavy team.
Movement speed Quints - These are another option for WW. He will be able to travel between camps faster as well as help his ganks. His bloodscent makes these a bit redundant later on in the game as you will probably be moving faster than everyone else already anyway. Attack speed quints are probably still preferable due to sustain they give.
Best Answer
Here is a guide created by a pro player for Shen on top lane runes, masteries, and items.
OR
It's really up to you on what quints you like using. Both are viable.