The Humble Store is a digital distribution solution from the team behind the Humble Indie Bundle. On November 11, 2013 the official Humble Store was opened, however not all games sold through Humble widgets have migrated to the store yet.
Games can be purchased via the developer's website (e.g. VVVVVV) or sometimes by going to https://www.humblebundle.com/store/GAMENAME (e.g. https://www.humblebundle.com/store/bittriprunner).
Content included with a purchase depends on a per game basis. For example, Gish only includes a direct download for the game, whereas Legend of Grimrock contains a Steam key also and Retro City Rampage pre-order contains the direct download, redeemable key, mini-soundtrack, printable NES label, digital manual and a 20% coupon for their store.
Games purchased via the Humble Store widget appear in the Humble Library (available from https://www.humblebundle.com/home), alongside any Humble Indie Bundles you have purchased with the same account.
Use a different payment method, e.g. after using PayPal for 3 keys, switch to Credit Card or Amazon payments.
The list of games that use the store is uncertain, though many can be found by searching for "Humble Indie Bundle, Game" in Google. However, according to Jeffrey Rosen all games in previous Humble Bundles had store pages created for them so that they could see what a widget would be like. This means that some are intended to be private and not used by general consumers.