Marks: Greater Mark of Desolation

Seals: Greater Seal of Vitality Greater Seal of Vigor Greater Seal of Replenishment

Glyphs:



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.



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.

Magical dmg:

Marks: Magic pen. Armor or MR is good for some defensive casters.
Seals: Mana-reg/lvl.
Glyphs: CDR or AP/lvl.
Quintessences: HP or AP. Magic pen is not adviced unless you've got bad AP ratios.

Physical dmg:

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.

Hybrids:

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.

Tanks:

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.