Broadly speaking the choices for page layout are between a corporate style and something more free form such as our Unfair Trade: Slavery site - or maybe an intermediate solution such Matt Biggs' H2o-StormGallery site.
Sometimes the more funky designs require the visitor to do a bit more thinking about how to navigate the site, but in the case of "Unfair Trade: Slavery" the layout gives the impression of having all the main content on one page, with each topic just a click away from the initial view.
The corporate style is formed with a top image band, including a logo, main navigation horizontally below it, and further navigation either vertically on the left hand side or as drop-down menus from the main navigation headings. Individual page content is placed in the area below and to the right of these areas. Occasionally secondary navigation is moved the right hand side of the page, and main content is moved to the left.
Footers are quite often used, particularly on corporate sites, for navigation to less visited pages such as terms and conditions, and site maps. They are best suited to scrolling pages, as on fixed height pages footers are an additional restriction on the area available for the main content.
Page length, then, is another important consideration, particularly where a lot of data is to be carried on one page. Where scrolling is inevitable the choice is between scrolling the entire page, or scrolling only the page's main content. Matt Biggs and I favour scrolling only the content, partly because his page designs are preserved, and partly to retain full navigation from the page at all times. Many modern designs scroll the entire page, however. My view is that usually a greater number of shorter pages is preferrable to fewer longer pages, and that scrolling is best avoided where possible.