Originally Miencraft, then terraria, Starbound and finally Shovel Knight.

Starbound still has to deliver more though.

Indie is a contraction of the word independent. We cannot connotate any small game with that word.

That's why Xbox Live has a marketplace for "Arcade Games", which labels small digital titles backed by bigger publishers. Games like: Shadow Complex from Epic Games or Splosion Man from Twisted Pixel.

And then in the same marketplace there are Indies. Games which are published independently by the developers.

Then find a new word...what does "indie" tell you about a game? Pretty much nothing. What use is such a word? I took it on faith that the OP didn't really care whether or not a game was technically independent, but that they were talking about the smaller scale that are typically associated with "indie".

The fact that the OP included Rain in their list pretty much confirms that they don't really care whether a game was published or not. Take it up with them...

Man, nothing fits the answer better than Minecraft. That thing exploded into one of the biggest games ever... o:

Probably the one indie I rememebr plaing late 2010/early 2011 back when I was invited to beta test G+ from a friend, made loads of friends during the 2011 mlp craze, didn't think MC would get so popular in that year alone when I was on one of the biggest FIM fan servers, all good fun in the end and something fond to look back on.

I think someday I'll built Walt Disney's Epcot park on some server sometime since it's my most favourite of parks =3.

The Swapper.

Ended up being one of my favourite games of last year, even beating out the likes of Shadow of Mordor and Hyrule Warriors.

I was initially intrigued by its eerie style that hearkens back to films like the original Alien, and by its interesting mechanical premise, but it went way beyond my expectations and is one of the most clever, atmospheric, and thought-provoking games I have ever played.

Gunpoint. It opened with a rainy level. THAT'S how to suck me in straight away. I looooove rain in videogames.

Transistor. Amazing. I think it's actually one of my favorite games of all time.

Flower.

Braid. Hard but rewarding.

Journey...when I play it.

Yeah, I avoided it for a long time, because I knew it was a game made for me, and I would lose several hours to it. I gave in, and yeah, I spent a lot of time on it... I haven`t played it in awhile, but I would like to go back and make a design I`ve had in mind for a long time x )

You're definitely right about that and I probably should've made my definition a little clearer and perhaps done some better research about the topic before I posted. Call it ignorance on my part concerning the topic, but basically I was referring to any of the "smaller" games or bigger games by smaller studios, which perhaps Rain fits into neither category and was a bad example on my part. I used the term "indie" very loosely as you can see and didn't mean to cause confusion. 

Thanks for your input, btw and again to everyone else. I'd forgotten how many awesome "indies" there were out there. Many of those mentioned here I've played, but there are far more I haven't so I appreciate everyone's input.