I have 3 main folders:
1) Layouts
2) Pictures
3) Scrapping
I will say upfront that I am an ACDSee girl. So all my tagging is done in ACDSee.
1 --Layout is pretty self-explanitory. I have one folder for the layered files and one folder for the web version. At the end of each month, I delete the web version (my own little form of house cleaning

). I leave the layered file on my ehd until I print. Then I burn it to DVD and remove it from the ehd.
2 --Pictures have a folder for each year. Within each year I have a month. I've been through Stacy Julian's Library of Memories, so this is my "category drawer" stuff. I use tags to tag all my photos. I only keep 1 prior year of photos on my ehd. Everything else is stored on a second ehd. When I want an older photo, I just plug it in and grab it from there.
3 --Scrapbooking. I organize by designer. I have one folder for New Stuff, with sub folders for each designer. This is where I put new kits that have not been backed up. Once I have backed up, then I move the files to the designer's folder in the main area. I also keep one folder for stores that do collabs (Like SSD). If there is a Two Scoops or Triple Dip, I just pick one of the designers to put the file in and call it good. Again, since I use ACDSee, a lot of times I'm using that to look for specific pieces, rather than looking for a kit.
I try to tag my kits as I unzip them...this leads to less frustration down the road when I can't find something I know I have

I think you are wise to think about organization now, before it gets out of hand. I still have some designers that are not tagged, but I'm working my way through it.