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A while back I saw someone asking for advice and a guide on what runes to buy once they reach level 20. A friend asked me the same so I decided to do it myself.
As of february 11/2010
My recommendation on what to buy if you don´t want to read my long explanation (this assumes you will only buy tier 3 runes as is the most logical choice) is:
Marks of Insight(+Magic penetration)
Seals of Evasion (+Dodge)
Glyphs of Shielding (+MR/Level)
Quintessence of Fortitude (+HP)
After you finish that get in the following order:
Marks of Desolation (+Armor penetration)
Seals of Vitality.(+HP/Level)
Glyphs Of Focus (+CDR)
If you want to have a more depth explanation or want to know what to get after all that, read the following.
Marks of Insight(+Magic penetration): Desolation Runes aren´t even terrible on casters, but insight marks are certinaly better.And I think DPS benefits more from Insight marks than some casters benefit form desolation marks. So if you have to decide between these two, i would certainly go for insight marks, but if you are sure you will mostly DPS in the future, get Desolation marks instead.
Marks of Desolation(+Armor penetration): These are probably the best option DPS have. They increase their Early game output damage by a lot. Game are about early game-mid game mostly. And this greatly increase the power of your DPS in those stages.
Marks of Furor(+Critical damage): Im not into this runes. I just happen to name them because they are very popular. Maybe someone can come with a wonderfull explanation on why you prefer this over desolation/insight in Gangplank or Tryndamare. But as for now I would say keep away from this. Yes In the letagame they increase the damage output more than desolation runes in some champions. But generally is early and mid game where dps needs help.
Seal of Evasion(+dodge): Flat out nuts the best seals. They Do not have diminishing returns unlike armor. They give a pretty nice amount of dodge. And if you happen to have nimbleness more to it. Also, unlike armor seals, wich do not go well with high armor items , etc. Dodge do not have that problem.
Seal of Vitality(+Hp/Level): In some champions build, this runes are better. If you aren´t going over 2000 hp anytime soon this runes are superior. Not only against magic, but even against physical, they are superior than every other seal option. So even if you plan to go slightly over 2000 hp at level 18, this runes are probably better than Evasion runes.
Seal of Clarity(+Mana regeneration/Level): I have to name them, because for what they do, they are great. The problem is that they are fighting with 2 great runes out there, and is a matter of opportunity cost. Getting these means you are not getting Vitality or Evasion, wich I will say are better. I wanted to name them because they are great. But for now, I think in most champions the opportunity cost is too big. I could consider them if you don´t go mediation in masteries. (Why you would do that?). maybe they will have a place when the masteries are reworked.
Glyphs of Shielding (magic resistance/Level): They Give the really needed Magic resistance. And it gives a ton, a full set gives 24 Magic resistance at level 18. Not based on the indivual champion needs this ones give the most amount of improvement stat wise. And it really helps to survive the mid-lategame AOE that flies in teamfights.
Glyphs of Focus (Cooldown reduction): I find this runes to be good in general. Some champions really want some cooldown reduction, but prefer to not invest gold in it. Too many champions ¨surviving more¨isn´t as important as ¨doing more¨. Most ranged nukers would prefer this to shielding imo.
Glyphs of Clarity (Mana regen/level): I find this a very situation rune. But let´s say that you don´t want to put points in meditaton (again i don´t know why) , you may find this runes to help you there and be better than the other options. Still don´t expect this ones to solve your ¨I don´t have meditation¨ problems.
Glyphs of Warding (Magic resistance): In some champions, depending on how you play them, you may prefer early game survivability. And this may be better than shielding in those cases.
Quintessence of fortitude: I think this are the most general and better runes. The amount of flat hp they give is insane. And while there are other runes out there, i don´t see how any of them match the raw power of this one. It increase the early survivability by a ton, especially on some nukers and dps that start with very little hp.
Quintessence of Swiftness: In some champions/build combinations where you have a lot of HP early on, even more hp won´t make that much difference. The second rune option is probably swiftness. It has a noticeable effect and they are decent overall. Some people like them too in ashe and other´s ranged champions.
I have yet to be convinced that other Quintessence are better options that the ones presented in some scenarios. But Im open to read explanations.