David,
This is always a difficult thing to do. If you use the meta data tags for keywords and stuff, and also have a tool that searches those, it can be a bit less daunting. If not, there will always be some shots "lost" in other folders, relying upon your memory to find them.
I am an event shooter, so storing stuff by date is more logical, but even there, I do break things out by subject or location. For example, I shoot wildlife at a nearby state park, so it gets its own folder, but then subfolders are done by date, and sometimes by subject, such as Brazos Bend SP > 061508 > Alligators, or Shore Birds, etc. Could just as easily swap those folders/subfolders to become Brazos Bend SP > Alligators > date, or type (close-ups, breeding, feeding, etc.) where date may be less important.
A lot really depends on what kinds of things you shoot, and how much you shoot of them, as that gives you some idea of how finely you may want to divide subjects in sub- or sub-sub-folders. I also rename all of my files to start with the date, so even if they are redtributed into other folders, I will at least know what season things were shot.
I use Aperture on my Macs, and am still mapping out the keywords and stuff I will apply to images for searching. The nice thing here is being able to leave all the images in whatever folder they started (by shoot date), importing things as referenced files, and then tagging keywords to those and rearranging their locations within Aperture, not the original file folder structure. Not sure if there is a similar capability in LR, since I do not use it. The nice part about having a fairly clean folder structure is that you can then access it by any other tool, such as Bridge, C1, etc. The downside to being too defined with subfolders is dividing things out in a way that may make it really hard to find anything after a while. This is the real plus of a good DAM tool like Aperture, since it will let you search for things in so many ways....as long as you tag the keywords for it to search. That is where placing "birds", "sunsets", "ripples", etc., into the keywords will let you find things more easily. If you do not use the meta data, breaking thing out into the folder structure you suggest will work for you, but you will still run the risk of forgetting where some things may be located. Different folks recall things differently. I tend to think about each shooting session as its own package, even if it covers more than one subject. If it covers too many, I usually break things down within the shooting session (event date) as subfolders. But that is how I tend to recall things. Placing all "sunsets" in one folder will work also, but I prefer creating those collections on the fly with the searches from the large database of images in Aperture.
Doing good DAM has components of both technical structure, and personal preferences in it, so no one method is best for all.
LJ