Apart from the templating stuff already mentioned:
Look for classes called .style1, .style2 etc in the CSS.
<p> </p> in the HTML source is another common giveaway, as are structural <br>s.
Scripts that start with "MM" such as MM_preloadImages is another common one as these were built into Dreamweaver.
People that use WYSIWYG usually aren't very fluent with CSS (or they wouldn't need to use WYSIWYG for layout/design) and this is often very apparent looking at the stylesheet.
Look for longhand rules that have been added to the stylesheet by the WYSIWYG like:
border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #FFFFFF;
Instead of border-bottom: 1px solid #fff;
Rules like "background-repeat: no-repeat;" are a giveaway.
Usage of six letter hex codes for greyscale colours instead of three is another indication, as most people hand coding would not bother but editors don't try to use 3 letter codes.
Something else I notice repeatedly (but can't explain why) is poorly thought selector schemes, in particular where almost every element uses a class of "generic_content" or "generic_paragraph" etc instead of using an element selector to set how styles should appear by default.
If you see selectors like (real world examples from a commercial Dreamweaver built site):
.genericTableB .blankCell (lol)
You are most likely looking at a WYSIWYG created site (or someone who seriously misunderstands how to use CSS)