Humble Bundle is one of the most popular, they usually run a weekly bundle, on top of a big bundle that runs for two weeks, as well as mobile/book/cd bundles, as well as a discount store. They also give away free games every once in a while.
IndieGala is another popular site, they run a weekly bundle called "The Every Monday" bundle, on top of other bundles they put together all the time. They too also have a discount store and give away free games a lot.
Bundle Stars is another I know one, they team up with PC Gamer a lot to give away free games from time to time. They run some interesting bundles now and then, as well as a discount store like the others.
Groupees is another good bundle site, they are known for "Build your own" bundles, where they will list a bunch of games you can pick and choose from and build up your own bundle packs.
Here are some others that I know of, but have never personally used.
Indie Royale
Bundle In A Box
Flying Bundle
Lazy Guys Bundle
I know there are others out there, but those are just the ones that come to mind.
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You forgot Daily Indie Game ;)
They run several bundles and also have a daily-ish game deal
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Bundle In a Box is long dead.
IndieGameStand's daily deals are sometimes worth it too
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Cheapest bundle that money can't give you! TheFreeBundle
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blinkbundle.com sometimes have decent steam game bundles too.
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nope, just forgot to put http:// into my linky, fixed now
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I keep track on bundles with isthereanydeal covers most of them.
The EpicBundle Group on Steam also does a good job imo.
Others then the ones already mentioned i have nothing to add.
Thanks to SvAlex for sharing ;) There are some i did not know jet.
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I don't know a lot of sites with games bundles, if someone could help me a bit i would appreciate it! (i use humble bundle, bundle stars, and indiegala)
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