'Independent' game development, in the case of Valve, is tough to define. Fez and Super Meat Boy are independent as the development process was funded by the developers themselves, versus publisher backing. But that can also apply to Valve. Portal was made using Valve's resources and finances, and Valve is a privately owned corporation. What's the difference between two guys making a game with their own money, and a hundred guys making a game with their own money?
It's a bit of a grey area in the case of Valve, because they're so successful and large as a corporation, yet public/external financing isn't applicable to their operation.
I should note with my rant above that I'm not discrediting Fez as a game, or any other 'popular' indy games. Super Meat Boy is a triumphant platformer in my opinion. Brilliant design. I quite like Braid's level design too. People seem to enjoy a lot of Fez, so for all I know it's amazing.
I just dislike the way the indy 'scene' perceived certain developers over others. In my imaginary world indy development should simply be people with aspirations, experience and passion for game development getting together, sharing ideas, philosophies and knowledge to help better their own work as well as the industry. They should be a collaborative entity that intends to serve the positive side of game development in opposition of the destructive business side. What it shouldn't be is a pissing contest of egos, and sadly this is what I feel it too often is.