Unless you're going to have something with full videos and very large displays, like a movie website, I would recommend against using Flash.
http://www.useit.com/alertbox/20001029.html
Good advise, although it's 10 years old, and its own design doesn't lend well to the alternative. There is some awesome stuff you can do with JQuery, HTML5, and CSS. I would recommend going towards that, unless you have a good team of artists that can supply the content for Flash.
That being said, here's a page with some good Flash sites:
http://www.ebizmba.com/articles/best-flash-sites