The major difference is that Microsoft wasn't actively working with the various web standards groups to standardize its various proprietary features. The majority of the non-standard functionality that's added to WebKit and Gecko is done with the intent of moving it on to the standards track if it is beneficial to the web platform.

Edit: If you can't see any difference between the approach to standards taken by Microsoft with IE 6 and by the people involved with WebKit, I'd suggest reevaulating your own biases.