Issues of Style
Once you've validated your HTML, CSS, accessibility, and links, and considered privacy, spamming, and other security issues, then you're ready to begin thinking about a well-designed web site. First, start with proper language use. Use a spell checker. Use proper grammar. Use clear prose. Use parallel structure but don't get too repetitive;-). Not surprisingly, here's a button -- Spell -- for spell checking. The bible of style, of course, is The Elements of Style. That tome, plus others on English usage, are available on Bartleby.com, a tremendous source of reference material. One other excellent site worth mentioning is Charles Darling's Guide to Grammar & Writing which not only presents information in a way that is easy to find, but also allows you to submit questions for things you cannot find on the site.
After language style there's web style. The best guides I've found for this are the Yale Web Style Manual. and UseIt.com the website of the guru of GUI, Jakob Nielsen. There are many, many others, but these clearly stands out from the crowd. A useful tool for reviewing the interconnectedness of your website is Mapuccino from IBM. This unique tool lets you interact with a site map which it generates for your web site, displaying the map in several different formats, and allowing you to zoom in by just dragging your mouse.