A good example of the issues plaguing search engines is the Graham Highlanders website. I designed the site with Bill Herreid when I was in high school. After completion, it took months for it to appear on Google. However, now that the band's clients have had time to find the site and place links to it on their pages, It is now the top hit for "graham highlanders" and has a page rank of 3/10.
All websites need a plan for how they expect to generate hits. I'm not talking about scams where you pay for a ranking; I'm talking about interested visitors. My personal site is listed on my business card and resume, and appears by my name everywhere I post content. My blog is categorized, tagged, and listed by Technorati. In this manner I generate the hits I want.
If an average visitor wants to reference your site, he wants to get in, find his information, and leave in under 30 seconds. Badly labeled sections, flash intros, loading screens, ambiguous navigation, navigation that relies on large pictures, and complicated sitemaps can bog the user down so much that he may look elsewhere for information.
When organizing the logical structure of your site, try to make your indexing as obvious as possible, to avoid ambiguity. Then, take a second look. If a user has to go through more than three consecutive links or has to scroll more than two page lengths to reach his information, simplify. If that's not possible, add a search function.
When creating page layouts, think. Are there any large images on a data rich page? Do you have to pass through pages with large graphics to get to data rich pages? Is anything in my site slowing down the user by its very nature?
Rethink flash intros and complicated animations.
Retool your interface to run faster.
Reconsider a search option.
Internet Explorer is the most prevalent web browser. It has many nifty features such as ActiveX, Microsoft filters, IE Behaviors, and Jscript. Internet Explorer displays images, applets, flash, and some proprietary security protocols. However, Internet Explorer is not the only browser. Hundreds of thousands of people use browsers like Firefox, Mozilla, Opera, Safari, Konqueror, Lynx, and a multitude of others for limited platforms and disabled users. These people should not be ignored. If you design only for Internet Explorer, you are going to severely limit your user base.