I've been using Arc and I've become a fan of folders + vertical tabs also. But I also want bookmarks with tags. I don't want to keep 'pinouts for xyz motherboard' open somewhere all the time. I want to tag it with 'dell', 'motherboard', and 'pinout' and then search when I need it instead of having to remember what 'Space' I put it in. I prefer bookmarks to web search when possible because often enough I spend stupid amounts of time searching for a little tidbit and may want to come back to it later.
Rather than cleaning out bookmarks, I would keep a few main bookmarks and folders on the toolbar, and file away everything else under one few big folders with tags.
I use Firefox for tagging and it seems to be a fantastic way to keep track of thousands of sites with small cognitive load. Am I missing some workflow that's 'better'?