Wow! It's been nearly 3.5 years since I started this topic... and it's surprising that not much has changed. The sites I mentioned as being good examples are STILL good examples!
I'm currently in the process of working on a new design of my own company website and I'm finding it hard to come up with something fresh, new and interesting that hasn't been done before. As a web design company the site has to show off everything that is great and good in the industry: Accessibility, usability, good design, quality graphics, well presented text and great content.
I'm following one of the other tips on here:
Design from the internal pages out to the homepage.
Too often I've designed a homepage and nearly completed a site for a customer only to be presented with content and images that won't fit... So for my own site I'm making sure everything works from stage 1.
I'm glad that lots of people have found this topic useful. There are only a couple of points that need to be added after all this time:
1) Accessibility and Usability - make sure your site can be read and used by everyone. Not only is it a legal requirement (UK and US) but it helps your site in every area including SEO.
2) Test, test and the test again on every browser you can get your hands on including PDAs and mobile phones. Over the next year or two there's going to be a huge increase of web customers using these devices - be prepared now and you won't miss out!
And that's all I can think of for now!