Web metrics firm Compete has an interesting post, outlining the top 20 websites (for US traffic). According to Compete, all 20 of them got over 20 million unique visitors in October 2006. Here is the chart:
A couple of people noted in the comments that if you add Microsoft's 4 top 20 properties together (msn.com, live.com,microsoft.com and passport.net), then they would probably be number 1. However a counter to that is that a lot of passport.net domains currently re-direct to live.com. I think there may be some crossover between live.com and MSN too. So it may well be that Yahoo remains number 1, even accounting for Microsoft's multiple brands. Plus of course Yahoo and Google both have separately branded properties too - e.g. Flickr, YouTube. If I was to estimate, I'd put Microsoft at number 2 overall - but interested to hear what others think.
Looking at the Alexa data for US traffic, the top 20 is quite different:
The Alexa list is (I think) only counting US traffic, but it is quite different from Compete's stats. The presence of non-mainstream web 2.0 sites in Alexa's top 20 (blogger.com, digg, flickr) suggests that the traffic is heavily skewed towards technical users - which makes sense, given Alexa relies on toolbar downloads to get their stats.
Also interesting to note there is just one Microsoft property in the top 10 in Alexa, compared to 3 for Compete.