If you want to search through just your bookmarks, you’ll be interested in this quick tip from Apple.
First, click on the Show All Bookmarks icon in the top-left corner of the Bookmarks Bar. Doing this makes the Collections column visible on the left side of Safari, but more importantly, it adds a Search field at the bottom center of the Safari window. When you type search terms in this field, it searches just within your bookmarks, so you get super-fast results.
quicksilver is also able to search your bookmarks, without even opening safari. one of the trillion reasons i love it and could never live without it.