You get skill points from the following:
1. Every level past lvl 20 you get 1 skill point
- every 15K xp I believe
2. Completing mission's that you get xp from, you will get skill points from them..
In Nightfall & Faction's..
1 skill point for normal completion,
1 skill point for expert
1 skill point for master's
In Prophecies - 1 skill point for completion.
- according to GW Wiki, no skill points from completing bonuses in Prophecies
If you have already completed a mission, you won't get any more skill points from re-doing that mission - unless you only completed standard/expert and re-do it and achieve expert/masters, then you will get the skill point(s) for completing the extra bonuses.
Also note, you won't get skill points for completing mission's that are prior to where you enter the storyline - ie a faction's/nightfall character going to do the prophecies section will NOT get any skill points from completing the mission's prior to Lion's Arch (ie Great Northern Wall, Fort Ranik, etc).
If your doing mission's that you are getting xp for and/or getting the 15K xp after lvl 20 and getting no skill points, then there's something wrong.. and you should most likely consider contacting GW support for assistance.
www.guildwars.com/support/
The following GuildWars Wiki page should help out as well:
http://gw.gamewikis.org/wiki/Skill_point