I've used Powermarks (as mentioned above) for years. It's a few bucks cheaper than Linkman (at $25), and does let you save notes for URLs. Works with Mozilla, Netscape (don't know about Netscape 8 though), Opera, Firefox, MSIE, NetCaptor, and Maxthon (or at least used to work with MyIE2), and probably others.
The main thing I like about Powermarks is that its search is instantaneous. I have several thousand URLs in my Powermarks file, yet if I enter a string to narrow down the list of matching URLs, the list is updated essentially instantly with every keystroke. I have seen others that aren't nearly so quick.
Another one is
LinkStash. A long time ago, I worked with the LinkStash author on adding Powermarks-like search functionality. I never really used it to see how well it works (shhhh... don't tell.
), but it may be worth checking out, as it's "only" $20.