An obvious example to this is hungering arrow. Without a rune it offers absolutely nothing. You lose out on many possible effects by not using a rune, however my next one can give an idea of how the un-runed skills can still be useful.
Take elemental arrow for example. So you want a fast projectile, that passes through minions. Without a rune, it is a fast projectile that will pass through enemies hit, much like lightning bolts or screaming skulls. Now by all accounts it would probably be better to pick lightning bolts over the un-runed elemental arrow, but some people could justify using it over screaming skulls as the fear can be annoying and inconvenient, especially when it causes an enemy to run and bring back even more enemies with them. So without a rune this skill can actually be useful, instead of just being "generic skill minus x added effect." I do understand that there needs to be "progression" where you unlock a rune for a new skill, you have incentive to change, however I wish there were still some cases where choosing to use the skill without a rune gave some advantages.
Anyone else agree?