There really isn't a right or wrong way to define your workflow...but I do recommend putting some thought into how you do it, so that you don't end up with a huge mess of files.
This was my basic structure/workflow:
RAW files uploaded from cards to primary hard drive. They are put into a folder named for the date and maybe the event. (I also have separate folders for Photo shoots, weddings or personal photos etc.). I also have sub folders for the year. So if did a shoot today, I'd save the files in a folder: Photo Shoots/2009/06-08-2009.
Then I'd back up those files on DVD or secondary hard drive (or both).
I would use a program to quickly browse through and delete the obvious duds. I might even do this before backing up. Then I'd go through again and pick out the best shots and flag or rate them somehow.
Then I'd use my RAW software to adjust those images and then convert them to image files (JPEG, TIFF, PSD etc). These would be saved in a sub folder called 'work' or 'converted'.
Then I'd go into Photoshop and edit the images, either individually or in batches by running actions on them. If I think I may come back to these images, I will save the 'working' files as PSD with all the layers intact. These files are huge though.
Then I'll save same output files, either for printing, web viewing or for giving to the client. These will be JPEG files and will be saved in another sub folder.
So when I'm done, I may end up with several copies of some images, especially if I save multiple copies for different print sizes. I will eventually go back and delete the working files (because they are so large) and back up the finished images.
That is how I used to do it. Now, however, I use Adobe Lightroom and things are a lot more streamlined. The RAW files still get uploaded into the same file structure but then I import them into Lightroom where I do the majority of my work on them. If they do need additional editing, I'll open them in Photoshop. I don't need to save multiple copies because Lightroom is a non-destructive workflow. So any of the changes I make, including cropping, don't actually hurt or change the original image. Basically, the images in Lightroom become my working copies. I can still save output files for printing, web or clients (and that's really easy in LR).