Draw pictures.
Pencil and paper is a good place to start when you're brainstorming screen designs and navigational elements. Play with shapes and colors as a means of coming up with a distinctive look for your site.

Make a flow chart.
The simplest way to do this is to sketch it out on paper. There are software programs which will serve the same purpose. Essentially what you are trying to do is organize and visualize the structure of your site, first in terms of it's branches, second in terms of the specific pages within each branch. Planning this out ahead of time will make it easier to keep track of how you want pages to link to one another.

Develop a file naming convention.
Building your site will be easier if you organize directory and file names in a meaningful, consistent way. First of all, decide whether your file names will be upper or lower case. This may seem like a trivial detail, but it becomes very important when more than one person is working on a site. Mis-communication about paths to different kinds of files, or the way that files will be named can lead to lots of tedious corrections if links are created wrong.

Even if you are working by yourself it's a good idea to come up with meaningful names. For example, if you have small icon versions of a set of graphics, and a full-size set of the same graphics you might want to indicate which is which in the file names.

Decide on a specification and stick to it.
If you intend to use consistent navigation, and similar page layouts in different parts of your site, sketch this out ahead of time. Make it as detailed as possible, specifying the size of different parts of the page layout relative to one another. Writing this down when you are fresh will make it easier to function at 3AM.

Build Mock-ups.
If you're planning a site with complex navigation, forms, or other interactivity it might make sense to create a non-functional version of some pages as a first step. You can either make your mockup entirely in Photoshop, or create an HTML version without worrying about making the scripts or backend elements work.

Use templates.
Once you have sketched out the appearance of a particular type of page, you can actually create the HTML code. After a period of trial and error you'll arrive at a page style that you like. Save a version of this page (or pages) as a template, so that if you are going to make a series of pages in the same style you won't need to code them over and over again.

Find tools that suit you.
Some tools, such as Fusion or Dreamweaver are designed specifically for the creation and maintenance of large sites. If you prefer other programs such as BBEdit you will need to develop your own makeshift strategies for automating certain procedures. Try different programs when you have the opportunity.