Almost always I would choose HTML/CSS over Flash sites. Flash takes longer to load, and even though in some cases it can be only slightly longer, to viewers it can make the difference between clicking away before the site loads and staying on your site long enough to see what it's about. The exceptions for me would be when you really need to do something like Flash games. But basically I think, if you can do it in HTML then stick to HTML. Nothing annoys me more than someone using Flash to do what they could have done in HTML/CSS.
Also from an
SEO perspective, Flash will get you nothing. The search engines can't read it, so they have no idea what your site is about, or how to index it. So if pages are all Flash based you aren't going to be getting traffic from the search engines. That's just a consideration.