I have organized in different ways over the many years I've been scrapping.
Around 2007, after I'd been scrapping for a couple of years, I learned of a method involving folders for every digital element -- papers, ribbons, frames, alphas, buttons, etc, with subfolders for colors. It worked really well back when I was getting started because I got a lot of freebies and my collection was small. I really liked mixing and matching kits.
But in 2012 I began scrapping for designers and also decided to start scrapping for hire. And I left the one digiscrap store I'd been nearly exclusive to for the previous 5 years and started visiting several. So I needed to start organizing by store and designer. And furthermore, I had to have my scrap4hire-friendly kits separate from PU-only.
I managed to to reorganize almost everything, but not thoroughly. And then, another year or two later, I nearly dropped scrapbooking completely in favor of focusing on my photography. But I missed scrapbooking a lot and have struggled to get back into it. I've done much better this year, since I designated Sundays my scrapping day, but like the original poster in this thread, sometimes I spend too much time clicking in and out of folders and scrolling through a lot of files to find elements I want to use on my layouts. And much of my stash goes ignored. I do want to use it -- I have weeded out old stuff I no longer like -- I just have so much!
The best thing I've done for organizing is making my folder thumbnails be the image of the kit or alpha or whatever it is, so as I'm scrolling I can see what's in the folders without opening them. Of course, I can't see the tiny things like buttons and stickers.
I know I need to get better at tagging! It's easy with Finder on the Mac. I just need to get consistent about it.