Recently, I noticed that it was taking forever for a new Internet Explorer window to open on WinXP. For convenience, I always left the Favorites sidebar open, and I realized that having the sidebar open was slowing IE's launch time. I suppose that for each new window, IE was iterating through the thousands of links I have in the Favorites folder, many of which are still in the folder root yet to be categorized.
Since organizing the Favorites folder is such a major pain anyway, I decided to dump IE's Favorites and find a new bookmark manager program.
LinkStash is an excellent bookmark manager that works with all major browsers, including FireFox. It's fast, easy to customize, easy to manage, and integrates with the browser seamlessly. And I'm actually catching myself searching my local bookmarks before searching Google. Highly recommended.
BTW, after you import your Favorites in to LinkStash, go ahead and delete everything in your Favorites directory (you can re-export them later, if you want). Check out the performance difference in IE!