When I decided I wanted to create my own web site I knew I'd want an overall theme, or at least some consistent model for most of the site's look.  My goal was to add some small amount of useful content, some real information, to the Web.  Content is text.  Text is often (or was often) words on paper.  My theme became "marks on paper" -- various ways paper is marked for different purposes.  This would allow me to have a purely graphical front page, using small "samples" as links to the areas I intended to divide the site into.   Hence a fragment of music for the pages where I list my CD collection, an equation as an entry point to my musings about Science, etc, etc.  Where ever possible, I wanted the image to be personal in some way.  Most of the associations came to me relatively easily and were reasonably simple to execute:
Welcome (Introduction)-"Welcome" in my handwriting (font)
Mark (About me)-My Designature
Software-A code fragment for a Processor close to my heart
Art-My four birds tessellation
Science-The emulator equation
Language-A dictionary entry (with the associated special characters and marks) for a favourite word
Music-A fragment of music
Literature-A line from a favourite poem, in a particularly lovely font
Miscellaneous-A typical doodle
Links-A fragment of my HTML, in the form I usually see it

In addition there were some "housekeeping" links I wanted to provide:
Colophon (Including how to email me)-An "@", embossed
Changes-A calendar page
Frames-The page cut and folded to form a frame

My original design had each image on a suitable fragment of paper -- different colours and textures and, where it made sense, the appropriate type of paper.  I started creating a piece of lineflow (remember that?) for the Software link; "Lineflow"?
The links would be "randomly" placed on the screen...   However, in the end I abandoned the idea and just stuck with simple images drawn transparently on one background and in a vertical stack.

I get the whole graphics thing pretty much out of the way after the front page and stick mostly to text.

During the site's development, I decided Frames were a good idea, a useful aid to navigation (although not so great for bookmarking) but I didn't want to interfere with the main page's layout so I've made it as small and un-obtrusive as possible.  I also deliberately made it purely textual (although I played around a bit with the text's case and the counter is a graphic), in contrast with the main page which is purely graphical.

In all of this, I am hoping for Substance over Style.