Is there any reason to not rune skills? From their descriptions they simply add additional effects (fire, greater area of effect, adds teleport, etc) and don't suggest any sort of trade-off. They don't seem to lose any of their original impact, but I may not be noticing among the hack-and-slash action.
If you have a rune, it is always better to use it. Blizzard CMs have confirmed that there is no reason to choose not to rune a skill, it is merely an issue of what rune to use. Of course, you might still want to use a skill before you have unlocked any runes for it, since a non-runed skill can still be "better" that a different, runed skill.