Imho

Cognition 1 & 2
Alien and Zombie Shooters 1 & 2

I'd have to say Super Meat Boy. I'm pretty sure I've seen them many times already.

Off the top of my head:

The Adventures of Shuggy
Puzzle Agent
Anomaly Korea
Magicka
Jamestown

Admittedly, with the amount of IndieGala, Royale, Groupees, HB, etc bundles, there are probably dozens of games I've left out.

I'll just say the one that comes instantly to mind: Cognition Episodes 1+2.

Yep, this is what I was going to say too.

I didnt think it was in that many bundles....

Well, it was definitely something that spang to mind. Anyway, I'm sure the true answer can be found here.

Only lists two bundles. Both Humbles. Im sure Cognition has it beat.....

Yes, it was. Seen it a couple of times before. Lots. Must be "strategy".

According to Austrobogulator's link, SpaceChem has been in no fewer then six bundles, topping Cognition's four.

Hacker Evolution: Duality has also been bundled six times.

Hard Reset, Swords and Soldiers and Gemini Rue four times each.

Machinarium and World of Goo have both been bundled four times.

But just like Super Meat Boy, only in Humble Bundles. Humble also had that tradition that they would add the last bundle to the current one as a bonus later on, so while they did quite a few repeats, I don't think that's quite the same as a game appearing in each and every indie bundle around.

Steel Storm: Burning Retribution (4, all from different bundle providers)
Cognition Episode 1 (4, all different providers)
World of Goo (4, all humble)
Hacker Evolution: Duality (5 bundles, though once as a repeat of "last bundle" plus once in Indie Game stand)

I would say Reversion. I think I have it from at least four bundles by now.