I have to add my kudos to Matt and Pierre for taking the time to respond to these threads. They could clearly just refer users to the Google Webmaster forums rather than answering in detail here. For all the flack Google takes, I have to say that I'm encouraged that two senior engineers take the time to answer questions in a 3rd party discussion forum.

My SOP is to make sure first that all non-canonical versions of the home page (the page with the most value, usually) are redirected, then make sure you set your preferred address in WMT, then add the rel=canonical tag to capture all the possible versions of the home page that you can't think of. As a side note I also noticed (the hard way) that Google treats capitalization in URIs the same way as these examples so www.Example.com is treated differently (at least for link value) than www.example.com. Basically if there is a single different character in the URI then it's considered a different URI.