Your rune slots on a weapon are limited, so you will have to decide which runes are worthwhile and which are not. This can be a tricky question.
The Flame, Frost, and Lightning runes are straight element damage adds. They are useful in a large number of situations and I personally favor them over most other runes in most other situations. Besides the occasional baddie which is resistant to the element type you're using, they are always active.
Silverite and Cold Iron runes do extra damage to Darkspawn and Undead respectively. The rate of damage they add is double that of the elemental damage runes, so a grandmaster Silverite run does +10 damage against Darkspawn. These are not great runes for an everyday setup, but there are instances where you'll want to go back to camp and switch your runes out. For example, you fight many Undead in Redcliff, so packing a Cold Iron rune is a good idea.
The Slow and Paralyze runes have a chance to slow or paralyze and opponent, with the chance increases with rune quality. The chance seems low, so I don't generally like these runes, although a Rogue with a Paralyze rune can be useful.
Finally there are the Dweomer and Hale runes which add spell and physical resistance, respectively. Given the large number of items and spells in the game that can increase resistance or grant temporary immunity, I don't find these runes useful at all.