It has begun. I have worked on quite a few games this year, most, if not all of them independent developers, and so in the past you would not expect these lists to have anything to do with me. This is hardly the case anymore. Last year saw a huge number of great indie games make the cut on some mainstream lists, and this year is already proving to be no different, especially for the absolutely wonderful "Bastion". Every person who worked on that game is a fabulous human being, and it was a pleasure to be next to them at PAX '10 with Super Meat Boy.
The Binding of Isaac is up for several awards so far, but this is the first top-whatever list I have spotted it on, taking # 10 in PASTE magazine's top 20 of the year.