When creating your web site, you should first determine what you wish to accomplish. You may have goals about how much traffic you want, how you want to site to look, how the site will help your marketing efforts.
Once you have you have brainstormed your list of goals, you should list them in order of priority. Like anything else the strategies for accomplishing one goal may reduce your effectiveness in another area.
Some goals to consider are portability, useability, accessibility, compliance, validity, indexablity, appearance, performance, effectiveness, efficiency, up front costs, ongoing costs, time commitment, role assignment, clarity, ease of navigation, etc., etc..
Many best practices will accomplish several goals at the same time. If your code is up to date, valid, and well formed, you will accomplish several goals. Your site will be accessible, easy for the search engines to access, quicker to download, and easier for visitors to use.
However some strategies, particularly those involving search engine optimization, will conflict with your other goals. SEO experts suggest many links, flat directory structures, and other methods to increase your ranking. Some of these strategies will work but may make your site more difficult for visitors to navigate and definitely more difficult for you to organize and manage your site content.
Therefore have a set of goals or principles will help you keep your project on track and will help resolve potential conflicts down the road