I prefer to keep all my bookmarks in my a local file set as my home page.

This particular bookmark page uses Javascript to expand and collapse sections of the page so that you can add lots of links without adding lots of clutter. This also allows you to group your links in logical areas. Each section's state is stored in a cookie and is remembered between sessions.

This page is generated from a Python script and a text file which contains the sections and their links. You can download the Python file here along with the sample text file and the associated cookies Javascript file. Sample output can be seen here.

If you have the Greasemonkey extension installed then you can add this script to count the number of times you click on each link on your home page. Use this information to build up a "Most Visited" section on your page!