I use Firefox as my main browser. I also use IE and I'm trying Opera again. I'll leave the browser discussion for later... for now I'll just say that if you only use IE, and just because "it's already there", you should reconsider.
One thing I don't like in any of them is the bookmarks. In IE it's just ridiculous. In FF it's ok, but seems a bit slow to me. In Opera I haven't even tried. The main reason is, I want all my bookmarks to be shared between all of them. I want to be able to manage them easily. I also want to be able to back them without digging for locations or functions.
I must have 20 or more bookmark backups, somewhere. Pretty much useless. I don't know where they are, it's hard to find stuff in them, I'd have to import or look in the files...
Here's what I'm doing now. I have a folder called Bookmarks on my desktop. Instead of bookmarking stuff, I just drag-and-drop the URLs from the address bar of the browser to that folder. Then I file stuff in subfolders. To open URLs, I just drag them onto an open browser window.
This technique should pretty much work under any system, Windows, Mac OS X, Linux. It makes it easy to back up bookmarks, you can file multiple copies under multiple folders and most important it just uses built-in well-known systems to create and navigate. No learning curve or 3rd party software needed.