From the official awards website:
2009 is the eighth year of the Indie RPG Awards, in a changing field for indie RPGs. While the line of independent and non-independent games has always been blurry, that became even more blurry with the sale of Indie Press Revolution to DOJ, Inc. in the spring. Last year's Game of the Year, Mouse Guard, was controversial to some because it was published by Mark Smylie's Archaia Press. Mark Smylie had published his own Artesia comics and RPG under that label - voted Best Production in 2005. However, it was unclear that the collaboration of Luke Crane, Smylie's Archaia, and comic creator David Petersen should still be considered indie.