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For my post, I'm only going to discuss the Humble Indie Bundles in particular, though if anyone wants to talk about the other Humble Bundles, I'd be curious what they thought of those as well. And there's no reason things like the Indie Gala or Indie Royale can't be discussed too, though I'm not really familiar with those.

4 > 6 > 3 > 5 > 1 > 2

This counts BTA games, but not games which were in previous bundles.

My reasoning is as follows:

HIB2: Humble Indie Bundle really was the weakest of them... It had some decent games, but let's face it, none of them were great. Cortex Command shows promise, but it's still in development, and the Bundle-Within-A-Bundle was far more incentive for getting the bundle than the bundle itself. It's the only Humble Bundle with the Indie tag that I'd say I'm truly disappointed with.

HIB 1: Though the games were hit and miss overall, it was still a great introduction to the concept. Lugaru, World of Goo, and Aquaria all more than hold their weight, and pull the weaker games in the bundle along.

HIB5: I'm probably going to get a lot of flak for this one, but let's face it: As great as Psychonauts and Bastion are- and they are truly great- they were pulling the entire weight of the bundle. Limbo, Swords and Sorcery, and Lone Survivor were all about style over substance, and Amnesia really isn't anything impressive. Still a great bundle for those two games, especially if you missed out on Super Meat Boy and Braid earlier, but it was overall a disappointment.

HIB3: This is the first bundle that truly seemed not just good, but great. While it does have Hammerfight which is arguably the single worst game in any of the Humble Indie Bundles, it also had plenty of gems: Atom Zombie Smasher, Cogs, Crayon Physics, and VVVVVV were all great games. Also, And Yet it Moves and Steel Storm weren't half bad.

HIB6: Though not quite the best, I'd certainly place the newest one among them. Dust Force, Vessel, S.P.A.Z., and Shatter are all excellent games, and even the "weaker offerings" this time around- Rochard and Torchlight- are still decent, solid games. Wizorb and Shatter being in the same bundle seems like an odd decision, but with all the awesome games, I really can't complain.

HIB4: The big one... The bundle that set the standard for all bundles. With not only some of the best games to be packaged in the bundle, but also some of the best variety amongst those games, HIB4 is definitely the creme a la creme. Cave Story, Gratuitous Space Battles, Super Meat Boy, Jamestown, Night Sky, and Shank were all excellent games, not one of those left me disappointed... The only game I can really complain about is Bit.Trip Runner, and even that's by no means a bad game, it's just a somewhat bland game that misses the point of platformers.
4 > 5 > 6 > 3 > 2 > 1

Favorites from each were

4: Cave Story+, Jamestown, Shank

5: Bastion, Psychonauts, Limbo

6: Torchlight, Wizorb (Haven't played the rest enough yet to know)

3: VVVVVV, Steel Storm

2: Braid

1: World of Goo
Heh, I actually found 3 pretty bad. I don't have every bundle, but it's probably my least favorite of the ones I do have. Hammerfight is pretty bad, Crayon Physics is a bit meh, And Yet It Moves was annoying, and I never really got into VVVVVVV. I liked Cogs' aesthetic, but the only game that really stood out from that one imo is AZS.
I know you said you weren't counting games that were in previous bundles, but for me the HB6 is pretty damned stellar. The reason is the only game I owned out of the lot is Torchlight. None of the others, including the ones they just added. So this one is a real deal for me.

I bought some of the other bundles, but not all of them. As far as rating them goes, I'm not really good at that sort of thing and I haven't played all the games from them yet either, so it would be silly to rate them yet anyway.
1. Frozenbyte, because of at the time exclusive DRM-free Trine. I was extremely sick when I bought it and sincerely hoped I did not hallucinate the whole episode.

2. V, because of exclusive no-strings-attached Bastion and all-around awesomeness.

3. Introversion, for having the highest percentage of games I did not have yet.

4. Android 3, because of Spirits, an awesome game I had never heard of. Would be even better if I had a tablet.