The Commander format (née Elder Dragon Highlander) began with a bunch of judges entertaining themselves over the course of long, major tournaments, with cards that rarely saw play; Sheldon Menery in particular, who was at the time a level 5 judge although he has since retired from Magic judging.
As the format grew, the EDH Rules Committee formed, and they created "the" banlist -- while many groups customize the list to their own metas, and there is a different banlist designed for 1v1 play, the banlist maintained by the RC was the gold standard for EDH.
When Wizards wanted to get in on the action, they decided to let the RC maintain their autonomy, although they did need to brand the format, hence the name change to Commander instead of EDH. While commander is now a supported casual format, even to the point of being available for scheduling via the Wizards Event Reporter software, playable in Magic Online, and detailed in the Comprehensive Rules document, the rules of the format continue to be maintained by the RC.
The RC has synchronized their rules/banlist update schedule with that of Wizards, which helps to avoid confusion from mismatched information.
In short: The banlist posted on mtgcommander.net is the official banlist.
- Duel Commander, occasionally called "French" EDH. The Duel Commander rules and banlist are maintained by a separate group from the Commander Rules committee, and Duel Commander is not supported by Wizards in the way normal Commander is.