Okay from the top...
Gym ladder is a special form of League. In this competition, players are competing for the top three places on their league's ladder. This is done by players challenging higher placed players (up to four spots on the ladder) in a game of Pokemon-e TCG. If the challenger wins then the player above falls down a spot (along with any other players) so that the Challenger takes the player's place. If the defending player wins, nothing happens. The top three players goes to the City Championships.
City Championships are a simple age-modified swiss tournament to decide the best single-player and the best Gym Ladder team for the city. Any one can attend a City Championship despite not being in a Gym Ladder Team. Note due to lack of league in the region (say like the state of Colorado), Gym Ladder team may just fight in State Championships and there may be no Cities for that state.
In State Championships, it is a simple tournament to find the best player of the state. My "guess" for countries outside of the US, these will be Nationals in a way.
Now push all of those tournaments aside because they have nothing to do with the Challenge Series or the World Championship.
Gym Challenges are most likely ran by local Premiere Tournament Organizers. Back in 2002, most Gym Challenges only held the main event. Now with Nintendo, you can expect to see side events (like small GBA tournaments) for free (just like in our recent Prerelease events). No matter the case it is up to the PTO running the Gym Challenge to have side events or not. With Gym Challenges, players compete in their age division to win a paid trip to the Pokemon World Championship. Even if you don't win you still can get Pro Points that can accumlate for more chances to get to worlds.
Stadium Challenges are one to two day events held by Pokemon USA, Inc. that feature a series of side events along with the main event. It is of a gaming convention level of Pokemon Play. Again the main event is the same however there is a chance more than one player from each division gets the right to play at Worlds.
Now the World Championship... Last year was a blast and I think next year will be too. This is an invite only event and so far I figured out three ways to be invited (not necessarly paid your way there) (1. High Ranking in Modified Global Rankings 2. Lots of Pro Points (maybe) 3. Winning a paid trip from a Gym or Stadium Challenge). It is a highly competitve tournament that decides who is the great player in the world (for each age division).
Well that is all I can tell of Pokemon Organized Play plans, note I do not speak for POP, I only speak for myself and what I learned off of the advertisement on the Nintendo Power issue for december, the Card List from Sandstorm and speaking with Dave back at Origins, plus my own instinct.
So for quick reference Gym Ladder, City, and State Championships are entirely different from the Challenge Series and Worlds. And the only invite-only event is the World Championship main event.