this Gamasutra article, which is worth a look.
The controversy arose because the ARG was designed to reward the players with the early release of Portal 2; the amount of time the release would be moved up depended on the amount of time all players spent on the indie games being promoted by the ARG. This wasn't exactly clear to everyone; some people thought the game would be released early merely if enough people purchased the indie game bundle.
This was a rather complex ARG with a lot of moving parts, and the article goes into depth on how the plan was created and executed. This is a good guideline for creating your own ARG, showing what sorts of considerations go into it and how involved the process can be.
I applaud them for their ambitious and creative marketing attempt, even if it had some flaws. Even the controversy helped them, I think, by publicizing the promotion.