League-of-legends – When a rune or item says +x magic penetration, how is that calculated

Combining two runes will give you a random rune of the same tier. Combining 5 runes will give you a random rune of the next highest tier. You cannot combine 5 tier 3 runes at once (as there is no tier 4).

The rune combiner is random. It doesn't matter whether you combine marks, glyphs, seals, or quintessences -- they all work with each other, and the output can be anything.

The idea is that, generally, runes themselves are priced such that it is slightly cheaper to generate a tier 3 runeset from your old runes than by buying the tier 3 runes on their own. For instance, the level 1 +AD rune is 15 ip, while the level 2 +AD rune is 80 ip -- if you bought 5 of the level 1 runes, combined them, and wound up with a level 2 +AD rune, you would have saved yourself IP.

Unfortunately, as mentioned earlier, this process is completely random. If you have tier 1 and 2 runes, by all means, combine them to higher levels; the rune combiner is just a way to possibly recoup the IP you spent on runes you no longer find useful, but it cannot be counted on to give you what you want. You might luck out and combine 2 random runes into a +Dodge quintessence (very expensive!) -- or you might get a mana/5 Mark (with a tertiary stat, and probably not worth the IP cost of your combined runes).

It's very much a gamble, and you don't get anything exclusive from it, so use it if you need to get rid of T1 / T2 runes, and safely ignore it otherwise.

Magic resistance stacks additively, and is calculated via this formula (assuming positive MR):

Damage taken = Raw damage * (100 / 100 + MR)

25 magic resistance → ×0.8 incoming magic damage (20% reduction).
100 magic resistance → ×0.5 incoming magic damage (50% reduction).
source

Magic penetration is applied in this order:

1. Flat magic resistance reduction
2. Percentage magic resistance reduction
3. Flat magic penetration
4. Percentage magic penetration
   source

Magic penetration stacks multiplicatively. Void staff (40% magic pen) and the Arcane Knowledge mastery (10% magic pen) together equal 46% magic pen. source

We can see that the types of magic pen are very important, because buying flat magic pen (sorcerer's shoes) makes % magic pen (void staff) less effective. Unless the enemy has a lot of MR (ex: Galio), it's not worth it to buy multiple types of magic pen.

Compare some examples with a base MR of 30. With 0 magic pen, 100 magic damage does ~77 damage. With Arcane Knowledge, we ignore 10% of 30 MR (27 MR total) and deal ~79 damage. With sorcerer's shoes, we ignore 20 MR (10 MR total) for ~91 damage. With shoes and arcane knowledge, we ignore 20 MR + 10% of 10 MR (9 MR total), or ~92 damage.

We can see that for low values of MR, increasing Magic Pen provides very little gain. It also shows how effective flat MR is vs low amounts of MR, whereas percent reduction is not.

Now let's consider a large MR, say 200 and 500 magic damage. With 0 magic pen, that's ~167 magic damage. Arcane Knowledge reduces the MR to 180, or ~179 damage. Sorcerer shoe's are the exact same here. With shoes and arcane knowledge, we ignore 20 MR + 10% of 180 MR (162 MR total), or ~190 damage. If we add a void staff to these 2 (discounting it's bonus AP for simplicity), we get 200-20-72-11 (97 MR total), or ~254 damage.

It's safe to say at this point that unless the champion is stacking MR, you'll do more damage buying AP instead of Magic pen. A notable exception to this rule is Soraka, because her passive provides a substantial MR aura.

tl;dr: Runes, masteries, and sorcerer's shoes provide enough magic pen vs most champions. Only buy additional magic pen if the enemy champion has over 100 MR.