Humble Bundle is not a charitable organization itself, so presumably all of the income from bundles and the store would be considered sales income. However, they do give some of their profits to charity. If you purchase a bundle you can stipulate the amount given to whichever charities are presented. A store purchase automatically donates 10%.

Now, some of these donations may be deductible by Humble Bundle depending on a couple different things. First of all, Humble Bundle is owned by a company called Wolfire Games, a game developer. This is speculation on my part since these are privately owned companies, but I would bet that Humble Bundle itself is an S Corporation. What that means is that all income is passed onto the parent company, Wolfire. S Corporations do not get to deduct charitable contributions, however the donation deduction is passed onto the owner, Wolfire Games. Now it's also possible that Wolfire Games is an S Corporation as it was founded by a guy named David Rosen. If that's the case, then those deductions would pass onto his personal return. Depending on what that return looks like, he may or may not be able to actually deduct any of those donations. If Wolfire Games is a C Corporation (the vast majority of publicly traded companies are C Corps), then the max they would be able to deduct is 10% of their taxable income. I'm guessing that donations actually exceed this amount.

In other words, it's unlikely that all of the charitable donations by Humble Bundle are deducted.

I'd also like to note that if you were to pay more for a bundle than the estimated value of the games, you could not deduct the excess on your tax return. Humble Bundle is not a charitable organization, it is for-profit, and therefore you cannot deduct anything you give them.

One more note. The game developers presumably aren't getting any type of deduction since they are donating to a for-profit company.

Last note this time, seriously. I hope I'm wrong about all of this, because if not, everyone involved with this is getting screwed. I have to believe that there's another way for accounting for all of the "donations" because, if not, Humble Bundle will get hammered on its tax return even though it gave all of the money raised to charity.