ClickZ Networks "Already a valuable resource for small businesses eBay has also proven to be the most trusted company according to a study conducted by the Ponemon Institute andTRUSTe." The Ponemon Institutes didn't post the study on their website, but the ClickZ Networks article talks a little about their methodology.
From Forsee results "eBay is the one non-retail e-commerce company that is among the elite of the ACSI. Their score of 84 is among the strongest of any company measured in the Index."
The ACSI group publishes their results online, although some of the links are broken. Here are the results for Q4 2003.
Amazon's number are a little higher (88) than eBay's but we're growing faster.
I looked for Microsoft's Q4 numbers but the link on was broken.