The way a site is built is important in more than one way. Not only do you need a site which visually looks good and works well due to the coding, you need a site which works well across all browsers and on multiple platforms. Cross browser cross platform testing is as important as any other stage of a website's creation.
In addition to having the site work and look correct for everyone who views it, the code should conform to the latest web standard.
The way the site is built is also important when looking for a good placement on search engine results pages. When you have a column based layout where there is the main content in one block and perhaps news or a sub-menu to the left in a block.
It is best to code the site with the main content first even if the page layout doesn't reflect this ordering. Search engines usually read code top down and left to right. Therefore, if a site is coded normally, to get your main content prioritised by a search engine you must build the site coding the main content first, then force the other content to go into position. For example, Google looks at your site, you don't want it to see latest offers as your main site content, you want it to read the main content and prioritise your site according to that content as this is the main part of your business - it is what you are selling rather than related / interesting topics. As well as the coding structure of your site, it is also useful to think about how your titles come across. Titles should be in a heading tag with the most relevant title in the first level heading (h1) and then decreasing in importance working down from h1 as this is how a search engine ranks titles. I will talk about what search engines look for in more detail in a later entry.
It is always important to take several factors into account when building websites.
SEO - it is always important to think, how am I going to sell my product on my site? How am I going to get people to my site? How are search engines going to see my site?
Accessibility - Is my site accessible to all people? Am I conforming to accessibility guidelines set by the web consortium? Am I allowing viewers to have equal access to my site? For example, If the viewer doesn't have the flash plug-in installed are they missing out on any content?
Usability - How usable is my site? Is the navigation obvious enough and easy to use? Where do people look when they first load my site? Does my site confuse people when they first use it? On top of these basic factors you have to consider how well your site gets your message / product / services across? Is it obvious what your site is trying to do?