Capture the flag is a gamemode, that has been mentioned by Notch, but not added into the game. It has 2 teams, who try and steal the opponents flag from in their base. Some servers have created this, with plugins and redstone. Jeb said he may add flags, so capture the flag may be coming out soon.
Teams
In capture the flag, there are two teams, normally red and blue, and on servers, the flags are normally "crafted" out of red and blue wool. As the scoreboard system has teams, that may be something to get closer to capture the flag.
How the game works
Capture the flag is a PvP game, with two teams. You try and steal the other teams flag, and return it to your flag. If you are successful, you win. If the other teams captures your flag and returns it to their base, you lose. Capture the flag is a multiplayer game, so you will need to know the ip for a server with this game on it. You could even host capture the flag games on your own server if you have one, and you want to.