I found a cool way to deal with bookmarks...I set up a Word document and I place all bookmarks in the doc. When it reaches 8 pages, I start another doc and save the first. After 3 successive saves, I go back to doc 1 and run through all the links, saving the good ones, deleting the so/so. Takes very little space and time to do this.
Meanwhile, my Microsoft Office came with an application called One Note... I LOVE THIS PROGRAM. You can make tabs and copy projects on each page of the tab. This is for a project that I really dont want to lose. Take a look at it over at the Microsoft site. It's really cool.