To quote the PHB, page 276:
"DAMAGE ROLLS
- Roll the damage indicated in the power description. If you’re using a weapon for the attack, the damage is some multiple of your weapon damage dice.
- Add the ability modifier specified in the power description. Usually, this is the same ability modifier you used to determine your base attack bonus for the attack.
In addition, any of the following factors might apply to a damage roll:
- Racial or feat bonuses
- An enhancement bonus (usually from a magic weapon or an implement)
- An item bonus
- A power bonus
- Untypes bonuses"
So, you get weapon focus and similar bonuses on damage rolls. You do not get them for flat damage numbers, such as the bonus damage dealt by Cleave, or the miss damage dealt by Reaping Strike.
A few other clarifications of the issue that I've seen some confusion with:
1) Any attack that says [W] is a damage roll. Now, the [W] is only part of the roll - whether it is mutliplied or not, the other bonuses remain the same.
2) Critical hits are still damage rolls, even though the damage is maximized. It is still a damage roll - you are just replacing the dice with the maximum result they would deal. (However, since you are replacing them with the max result, rather than rolling the max result, it wouldn't auto-trigger the Vorpal weapon special ability.)
3) If you make multiple attacks with one action, each damage roll can get the effect of your bonuses. For example, a Ranger can use Twin Strike as an at-will power. He makes two attacks that deal [W] damage, but don't get his normal strength or dexterity modifier to damage. But they would each get the benefit of Weapon Focus, weapon enhancements, and similar bonuses.