I use Emacs / Org Mode for bookmarks. I use a few different browser profiles, and usually always want to open a bookmark in a specific profile. Having all bookmarks in one place is much easier than figuring out which browser I need and then finding the bookmark in it. Plus this way I can use other Org Mode features with them too (adding any arbitrary notes/tasks to them, todo keywords for a reading list, refiling/archiving, etc.)
Basically I just add the properties URL and BROWSER to any entry I want to be a bookmark. I have the numpad key 4 bound to a command that opens the url (works either in the org file buffer itself, or from an agenda view). I also have the numpad key 1 bound to an agenda search for the tag :bm: (searching for a property is too slow), so I can easily get a list of all bookmarks, which can then be filtered by tags, category, top-level headline and regexes.
Basically I just add the properties URL and BROWSER to any entry I want to be a bookmark. I have the numpad key 4 bound to a command that opens the url (works either in the org file buffer itself, or from an agenda view). I also have the numpad key 1 bound to an agenda search for the tag :bm: (searching for a property is too slow), so I can easily get a list of all bookmarks, which can then be filtered by tags, category, top-level headline and regexes.