I think a scaled back version of how you were doing it before would work. I don't have a single drive dedicated to my photos, so instead have a folder on my data drive called Photography.
My workflow is this (primarily working in Adobe Bridge):
1. I have a folder called Incoming where all new photos are put until I complete pretty much everything below. Within the Incoming folder I create a folder with a name that best identifies what the shoot is, and then a subfolder called raw. Sometimes the name of the root folder is specific (Elm Creek Church - all shots taken on or around their property), but sometimes it isn't as specific (Abstract - could be from anywhere), and sometimes after I've completed all the steps below I will move individual images from one folder to another if I feel they fit better in another folder. I have another folder called Texas Landscapes where I got more specific and have some subfolders as well, such as Elm Creek Church, Hill Country, and Other, etc.
2. Download files into raw folder within appropriately named main folder.
3. Do a quick edit to delete anything that should never see the light of day, or anything that is too similar to another shot and doesn't have any outstanding reason to keep it.
4. Rename the files using a numbering system consisting of 5 digits (starting from 10,000). In order to keep track of the numbers I write down the last number used in a notecard that I keep by my monitor and always reference that before re-number new photos (I also from time to time do a search for the highest number to make sure it only comes up as one image). About 1% of the time I will rename using a more specific name, but that isn't very often and isn't entirely necessary when the files are in an appropriately named folder. When I shoot a pano or HDR photo I will select the series of images and (in Batch Rename) manually type in the image number, then put a 3 digit number sequence on the end after a dash, so it would look like 12345-001, 12345-002, etc.
5. Do a hard edit, looking closer at each image to determine if it is a keeper, a maybe, or a delete. I will often open the maybe's and delete's in Photoshop to do a quick edit on them to see if there is anything redeeming about them before making my final decision. And even if some of the maybe's don't improve to keeper status that doesn't mean I automatically delete them. Sometimes if there is just 'something' about them I will file them for future toying with (such as the abstracts I created using photos of moving water that by themselves were only so-so).
6. Work on the keepers to make them the best they can be, or what I want them to be, depending on the image and circumstances. Combine HDR, stitch panos, color correct, dust, etc.
(6b. Sometimes I do step 5 and 6 in the opposite order, depending on the job / situation / my patience at that moment.)
7. I save all my high resolution edited files within the root folder, so for example in the Abstract folder the edited / tweaked photos are saved as PSD or TIF in the root of that folder. Some folders where the images will have various uses I have some additional subfolders such as JPGs, Postcards, Flyers, etc.
8. I have a few other folders for specific uses that any photos may end up in, such as 01 Temp for Posting, 01 For Online Shopping Cart, etc. The 01 is there so the folders show up at the very top of the folder list so they are quick and easy to get to.
Some other notes:
I often visit the same places many times so I used to get more specific with folders by including the date I shot the images in the folder name but decided this was overkill since sometimes I would only have one image worth keeping from any given date. There are still instances I will include the date in the folder name but it isn't very often (and usually a job related reason), and when I do I do it as a subfolder, such as a main folder called Hockey with subfolders 5-3-03, 6-5-03, etc.
If you adopt the number system for your file names you might need to start with 100,000 depending on the number of shots you take. I don't shoot a super high quantity of images since I am doing mostly my own fine art photography, I will wait and wait and wait for that one shot and after a whole day might go home with any from 20 - 100 shots (and I'm not shooting every day either). I also am pretty critical on my edits so even if I come home with 400 images I might delete 200 of them before I re-number them. But if you shoot a couple thousand images at a time and keep the majority of them, you will go through the 5 digit range pretty quick.
I very rarely will have the same files in more than one folder as that can lead to a lot of confusion (Did I use the same file name twice? Which one is the most recently edited? Etc.). In the past I sometimes would leave the files in the folder that related to the actual shoot (ie Brian Head) and copy a couple specific files into a different folder (Abstracts), but since I often go back and re-edit images after months or years I wouldn't always remember that I had it in both places. So I decided that if to me the visual impression of an image was better described by the Abstract folder than by the place it was shot, that the file should only be in the Abstract folder.
When I do a commercial job I will rename the files to relate to the job itself, so I don't use up any of the numbers in my 5 digit numbering system. But you probably already figured that since you have done commercial jobs.
As for tracking what you've posted online, I admit I'm a little lax about that. I have a folder on my FTP site called forums where I post 99% of the images that end up online. Lately since I've been using a blog as my primary website I've been using the links it creates to post images instead of uploading to my forums folder. For the most part I'm not too worried about it, a month in the online world is a decade in real life, so if I should delete something and it isn't available on some site somewhere, most people will never notice. That said, it's not often I delete anything from my forums folder since I have practically an unlimited amount of storage space. Now that I'm using a blog format that keeps everything organized and archived, until / unless that format changes I have no plans of taking down any of those posts.
And my blog / blog gallery is one of the ways I keep quick reference to my favorite or best photos. Sometimes a single image can get a little lost in a folder with 100 other images and while sifting through a folder in Bridge isn't that slow, if I know I'm looking for one of my better images then the odds are good that I have it in my online gallery and can quickly look up the image number there. I used to have another folder on my hard drive that was 01 Absolute Best (ok, still have it...but don't use it) where I would COPY (that bad word again) the edited high res PSD or TIF of my favorite shots. But again I decided that that level of specificity wasn't necessary when I had other quick references to those same images. If we were still running command line OSes then it would be another story...but we have pretty visual thumbnail driven programs that make it easy to see what we are looking for and are fairly quick even if you have a lot of images in one folder.
Now if you have thousands of images in one folder that's another story and you will have to ask Joe if / how he goes about tracking his favorites within those folders. The one method I'm aware of and have used on occasion is Bridge's star rating system, though often I do it backwards. I will give an image 1 star if I plan on deleting it, so after going through the folder I will set the filter to show only 1 star images and will give those a quick 2nd viewing before selecting all and hitting delete. I have on some occasions used it the normal way where I've given so-so images 2 stars and keepers 5 stars, but I'm so picky about my edit that often the images are either a 1 star or a 5 star in my mind, so I simply don't often use the star ratings. If you have a folder with thousands of images and want to separate a few specific images I would say give them a star rating to show that they matter more than the others, then in the future use the filter to quickly find them.
That enough info or you want more? Sorry, have to go to work, can't type anymore. ;)