If you haven't tried it yet, give My Yahoo! Search a spin. I work for Yahoo! so I'm naturally a little biased, but I truly love this beta service.
It allows you to create your own collection of sites to search in, and gives you various ways to organize them. It also lets you add any search result instantly to your collection, and can keep track of which search results you click through to.
Combined, this works better for me than most bookmarking tools, as I tend to bookmark far too many sites for it to be practical to maintain a folder structure. Now I only bookmark a few sites, and add the rest to My Yahoo! Search.