Not Updated For Current Season
Marks: Greater Mark of Desolation
Seals: Greater Seal of Vitality Greater Seal of Vigor Greater Seal of Replenishment
Flat stat bonuses
Marks, seals and glyphs give much smaller flat stat bonuses to most stats. So "per level" bonuses are usually better in these categories.
AP, mana-reg, HP and HP-reg are the bonuses that are much better in "per level" form. (unless you really need it early on)
Examples: Greater Seal of Scaling Mana Regeneration, Greater Seal of Regeneration and Greater Seal of Vitality all have over 4 times bigger bonuses than Greater Seal of Replenishment, Greater Seal of Vigorand Greater Seal of Health.
All those bonuses are normal in quintessences though. So it's a good idea to get them there.
AD, AP, armor, MR, mana, mana-reg, HP and HP-reg are the bonuses that are larger in quints. The biggest difference is in AP and HP though.
Examples: Greater Quintessence of Health and Greater Quintessence of Ability Power have over 5 times bigger bonuses than Greater Seal of Health and Greater Glyph of Ability Power.
Useful secondary runes
While most secondary runes are ****, there are some that give almost as big bonuses as the primary ones.
Example: Greater Seal of Scaling Mana Regeneration Greater Glyph of Scaling Mana Regeneration, 12,96/16,2 = 0,8. The glyphs only give 20% less than the seals. So these glyphs are worth getting with those who need mana-reg in glyphs.
Here are the good ones I've found so far:
I'm gonna state some good runes to have for different kinds of champions here.
Marks: Magic pen. Armor or MR is good for some defensive casters.
Glyphs: CDR or AP/lvl.
Quintessences: HP or AP. Magic pen is not adviced unless you've got bad AP ratios.
Marks: Armor pen, AD, AD/lvl, crit chance or attack speed.
Seals: Dodge, mana-reg/lvl or HP/lvl.
Glyphs: MR, MR/lvl or CDR.
Quintessences: HP, armor penetration, AD, AD/lvl, crit chance or attack speed.
Marks: Armor pen or attack speed. Magic pen is not recommended for those with Archaic Knowledge.
Seals: Mana-reg/lvl, HP/lvl or dodge.
Glyphs: CDR or AP/lvl.
Quintessences: HP, AP, or armor pen.
Marks: MR, armor or penetration. (penetration depends on what kind of dmg you mostly deal)
Seals: Dodge, armor or HP/lvl.
Glyphs: MR or MR/lvl. (are the best unless you desperately need some CDR)
Quintessences: HP, armor or MR.