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Determine the site's functionality. Create a site map diagram. Try some card sorting. Use paper and a bulletin board, or a whiteboard. Take a Content Inventory.
If you're making the site for yourself, you probably already know the answer to this. If you're making the site for another person, company, or organization, you'll need to find out what they expect from the site and its functionality. Everything you decide here will have an impact on the final website.  Does it need a storefront? Do you need user comments? Will users need to create accounts? Is it article-oriented? Image-oriented? All of these questions and more will help inform the design and structure of the site. This can be a drawn-out process, especially for larger companies with lots of people involved in the project. A site map diagram is like a flow chart and shows how users move from one page to the next. You don't even need pages at this point, just a general flow of concepts. You can use a computer program to create a diagram, or sketch it out yourself on a piece of paper. Use the site map diagram to show how you envision the web page hierarchy and connectivity. A popular method for a group is to use a stack of cards to figure out everyone's ideal approach. Take a stack of note cards and write the basic content of a single page on each one. Have your team organize the cards in the way that they deem most useful. This is best for situations when you are collaborating with others to create a site. This is the original low-budget planning method, and allows you to quickly erase or move content and reroute it. Draw the design on pieces of paper and connect them with string, or draw the outline on a whiteboard. Great for brainstorming sessions. This is more geared towards redesigns than new sites. Enter each of your pieces of content or existing pages into a spreadsheet. Make notes as to the purpose of each one and use this list to determine what goes and what stays. This will help cut the fat and simplify the redesign process.