While at one level, navigation and media, layout is tied to the site's paradigm, at another level, the aesthetic, it transcends paradigm.
Navigational layout is crucial, especially if the site makes extensive use of hypertext links.
Good navigational layout contributes to the overall feel of the site. The feel of the navigation is, in many ways dependent on the paradigm. Print-based sites will have a linear, hierarchical navigational layout, true hypertext and hypermedia sites will have a nonlinear web navigational layout. Media layout issues include the appropriateness of the media for the information to be conveyed. Too often I've accessed sites that seem designed for T1 connections, not 14.4 modems.