Since there's no DRM you can't help it if people are buying one key and then burning a bunch of CDs, but that won't affect the average price much. Seems to me that if they're selling license keys for $1.50, the best way to counter this is to change the download screen title to:

    Thanks for purchasing the Humble Indie Bundle #3 for $0.01!

... if the customer thinks that's fair, so be it, but it might at least encourage the "resellers" to pay slightly more.

Alternatively, I don't think setting the minimum payment to $1 would be at all incompatible with the "pay what you want" slogan & worthwhile if it eliminates the payment fees problem.

(But what would I know? I've bought all four, and last time 'round I felt like I got my money's worth just out of Braid.)

They seem to have cottoned on to this: if enter a price of less than a dollar, you need to fill out a re-captcha.

    Orders under $1 must authenticate with reCAPTCHA to help cut down on costly abuse.