If you have on demand television, such as DirecTv, Disney XD's On Demand Network has over six hundred episodes of the Pokemon anime available. Except season 4, and possibly season five. But they sometimes come back after the episodes expire. If you don't get on demand tv, this might not be of use to you, sadly.
But other than what I know, maybe your safest bet is the official Pokemon website.
Also, since some episodes are banned, such as the Jynx episode (Holiday Hi-Jynx) you might not be able to watch every episode in order, unfortunately...