The idea for the Humble Bundles was inspired by the fact that every Steam bundle sale seemed to automatically get to the number one story on reddit. Wolfire itself put their toes into the water with the bundle concept by bundling Overgrowth with Natural Selection 2, which received a decent amount of press coverage and attention on Reddit, garnering 1600 sales. Another source of inspiration was 2D Boy's successful pay-what-you-want promotion for World of Goo. This led Jeff and John to begin considering how to top a pay-what-you-want sale.
The ideas Wolfire came up with to make an even more compelling sale were to add more games, add support for Mac and Linux platforms, make a better site, add charity donations, and release the source code to the bundled games.
Initially, it was difficult to get developers on board with the idea, especially because they had to limit themselves games already supporting both Mac and Linux. Getting charities onboard was somewhat easier -- 10 minutes into Jeff's complicated pitch, the EFF representative stopped him and asked, "So, you're asking me if you can give us money?"
Wolfire also covered some of the challenges with designing the Humble Bundle site. The challenges they faced included making sure the site was scalable, easy to use, while also providing good customer service.
For scalability, as Wolfire has documented in their own blog, they utilized Google App Engine to host their site. At the highest point, they had 70 instances of their app running simultaneously across Google's servers, and had nearly perfect uptime over both bundles. Amazingly, Google only charged them $10.
They also utilized two CDNs for the actual file downloads. For the first bundle, they used Akamai, and for the second they used MaxCDN. They recommend Akamai, which they say is the most expensive service, but also the best.
As for the ease-of-use goal, they designed their web site such that you did not have to register an account, fill a shopping cart, get a verification email, require a special client program download, etc. There was only one pre-purchase page, and only one unique post-purchase page per user.
Customer service wise, they used the Tender service to track support request emails as tickets, as well as the Olark service to do customer service via live web chat. They only had 18 live chat operators total, and most of the time only a couple people were active, but they managed to handle many many support requests in parallel once they got into the proper mental flow.
The gentlemen from Wolfire then described the specific pre- and post-launch experiences for both bundles. For the first bundle, there was initially very little press interest (with the notable exception of Ars Technica), and only once they began approaching the $1 million sales mark -- the threshold for releasing the source code to the games -- did other press coverage begin taking off. The first bundle achieved $1.27 million in sales over 138,813 contributions.
For the second bundle, they were concerned whether the first bundle was a fluke or actually a repeatable phenomenon. To improve the bundle, they planned new features to improve it beyond the bar set by the first bundle. They added new games, including Braid which was ported to Linux specifically for the bundle, and Revenge of the Titans, which was actually launched for the first time inside the bundle. They also made plans with Steam, OnLive and Desura to provide download keys for the games in the bundle, allowing users to unlock the game on those services instantly, something that was only offered after the fact in the first bundle. Humble Bundle 2 ended up an even larger success than the first, with ~$1 million going to developers alone, another ~$500,000 going to charities, and $133,000 as a "humble tip" which went to support the Humble Bundle as a business.
There were some unfortunate events that occurred post-launch. For example, some customers bought a thousand copies of the bundle at 1 cent per copy, apparently planning to resell the games elsewhere. Also, an estimated 25% of downloads were pirated directly from the Humble Bundle site itself (via shared CDN links), not even counting BitTorrent or other channels.
There were some other issues. After open sourcing Lugaru, a counterfeit version built from the open sourced code appeared on the Mac app store for 99 cents, significantly undercutting Wolfire's own offering of Lugaru HD in the same store, even coming in ahead of them in search because of the shorter name. Another problem (which I do not recall being publicized as much with the Humble Bundle as when it occured with e.g. Minecraft) is that Wolfire also encountered the same dreaded "account freeze" where PayPal placed their balance under hold for an undefined period of time. Wolfire's opinion is that while they were very satisfied with Amazon's payment system, and Google Checkout is at least good for merchants, despite PayPal's unpredictability it is virtually required to support because of how ubiquitous it is as a payment method.
In total, both bundles made $3 million dollars, of which $1 million went to charities such as the Electronic Frontier Foundation and Child's Play.