Super Meat Boy, Cave Story+ and Machinarium are all from Humble Bundles, and I fell in love with each one as soon as I started playing them. i'd go as far as to call them my top 3 favorite games ever, and they're definitely the best games I've got from bundles. And know that I think of it, it got me a while to warp up to Psychonauts (from HIB V), but once I did (continued from where I quit last summer after I bought Double Fine Bundle) I enjoyed it more than any game in a long time. And then there's Bastion, of course. I bought it again with BTA price when it was on HIB Weekly because I absolutely adore the soundtrack, and I wanted to support Supergiant Games because their next title Transistor looks just as awesome as Bastion.
Some really great games I've enjoyed a great deal such as VVVVVV, Braid, The Binding of Isaac and Hotline Miami have been included in bundles, but those I've bought directly from developer or Steam so I don't think they count in this thread.
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VVVVVV! I pretty much played all of the games from the HiB 3 more than any other bundle.
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Many of my favourite Steam games came from bundles...
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Super Meat Boy or Saint's Row the Third. Both were the main reason for getting the bundle they were in.
Honorable mentions go to Cave Story+ and Jamestown
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My favorite would be Bastion overall, especially as it included the soundtrack. From the current bundle I like Capsized.
Edit: I also had a good time in Dungeon Defenders, although I got it before it was bundled.
Edit2: Metro2033 was also good.
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