The whole concept of HTML and CSS is to separate the content of a site, from the presentation. To layer it. This means that there should be absolutely NO content in the CSS, and absolutely NO presentation in the HTML.
Over and over I'm seeing sites with things like id="left" in the code. What happens when the design changes? "left" gives no semantic meaning to the element at all, that is presentational, and should not be used. A better way is to name it something relevant to the content it contains id="home-page-quote", etc. Now when the design changes, the HTML still semantically represents the content.
I'm also seeing the use of spacer.gif's. Back in the days of table based layouts, people would use spacer.gif files (a small transparent image) to space out the content. Not only is this very bad practice, as it will mess up the layout for people who use mobile devices, but also because when the page is viewed without style (such as for screen readers) there will be images all over the place that lend absolutely nothing to the content. If you use CSS, there is absolutely no need for a spacer.gif file, you can do everything you need in CSS, with no exceptions! Padding and margins can space out the content and you can use letter-spacing, text-indent or line-height to space out text.
Another thing I've noticed, is the use of a div which has class="clear", yet it has no content whatsoever. Again, these add nothing to the content of the page, they don't make semantic sense. This is presentational, as you want to clear a float. But again, what if the design changes? The markup will need to be changed too. It is possible to use CSS to make self clearing floats with minimal effort, and with valid standards compliant CSS. A quick Google search will reveal many different pages discussing the matter of self-clearing floats.
When viewing HTML without the CSS applied it should be in a suitable order so that it reads well, and only images which are part of the content should be shown (logos are included here, as they're part of the page content). If the page is in an odd order, screenreaders will be confusing for people and if random style images are showing, then it detracts from the content. You should be able to completely change the layout of a page by only editing the CSS. If you have to edit the markup, then you've done something wrong and need to re-think the code. This includes extra markup only used for presentational purposes. You shouldn't have a div called "coloured-line" for example, as this is specific to the current design. Yes, you can hide it in later designs with display:none, but ideally you want to make the coloured line just part of the CSS and give no reference to it in the markup.
Nobody's perfect, and I've done many of the things I've mentioned here in the past myself (and a lot more recently I've found myself naming classes "left" without realising until later). The whole point is that we find new and better ways to do things, and constantly strive for perfect code. Hopefully this will help some people to use HTML/CSS the way they were meant to be used.