is there an application to manage bookmarks? I hate the in-built book mark managers of all browsers, it quickly becomes too messy and important links are hard to find

Is there desktop application which deal with bookmarks? something that has multiple options of fitters: categories, folders, tags and more 

For example the task manager, omnifocus, is as simple or as complex as you want it to be, is there anything like that for bookmarks
Take a look at Xmarks. It stores the bookmarks on an Xmarks-server, so they are available from everywhere. It's compatible with Safari, IE, Firefox and Chrome.