Are all skills affected by elemental damage increase?

In Diablo 3, all skills have an element assigned to them (physical, cold etc.). What I'm wondering is what happens if a skill does not do direct damage? For example: Mantra of Conviction, Inner Sanctuary with Forbidden Palace rune. They apply a debuff on enemies that makes them take x% additional damage.

Is there a general rule telling when elemental% applies and when it does not?

Elemental % applies to every skill. If a skill does damage, it will have an element, and be affected by +Elemental damage of the correct type.

The skills you are specifically referring to have no element because they don't do damage. All they do is make other skills do more damage, and will affect the skills used while enemies are under those debuffs.