I have this problem happening on a new 2011 Macbook Air with the latest version of Lion. When viewing emails, the text is coming through as odd characters that look like a capital A in a box (see image below). If I click Reply, and then convert the message to plain text, the entire text of the email displays fine. But in the message list, preview pane, and full message view, I get the odd characters any time I'm display rich text.
I've verified that my Mail.app is up to date, and in the Fonts & Colors preferences, the message font is set to 12pt Helvetica.
I can't say for certain, but I believe this started after I installed a trial of Microsoft Office for the Mac. The entire office suite (including Outlook, Word, Excel, everything) was installed.
Best Answer
We went digging through FontBook and found a bad copy of Georgia installed by Microsoft Office. After going through about a dozen duplicated font files, and removing the older versions of each, we restarted Mail.app. At this point everything is working perfectly.