There are a lot of variations from the "standard" depending on champion and situation. One specific example is Thresh who runs ad marks armor / hp seals mr glyphs and armor quints, with the seals and glyphs swapping out of scaling ones depending on how damage heavy the lane is and how the lane damage is split between physical and magic damage
Hecarim
Greater Mark of Armor penetration
Greater Quintessence of Movement Speed
Greater Seal of Armor
Greater Glyph of Magic Resist
Rammus
Greater Mark of Attack Speed
Greater Quintessence of Armor
Greater Seal of Armor
Greater Glyph of Scaling Magic Resist
Mordekaiser
Greater Mark of Attack Speed
Greater Quintessence of Ability Power
Greater Seal of Armor
Greater Glyph of Magic Resist
Master Yi
Greater Mark of Attack Damage
Greater Quintessence of Attack Speed
Greater Seal of Armor
Greater Glyph of Attack Speed
Not sure if I missed any, and all these runes are my personal preference. Others might have other choices though.