So I just purchased Lightroom 4 and Photoshop CS5 (free upgrade to CS6 when it's released) and I am trying to establish a workflow and file organization system. So if others could share their methods, I think it would help me to develop mine.

Right now I put all my RAW files in one directory with subfolders organized by date. I save final metadata files to the same folder as the RAW file. I have a separate "Gallery" folder with completed JPEGs.

I don't have solid workflow yet, but here is the order I have been using:
-Lens correction
-Crop
-White balance
-Noise reduction
-Sharpening
-Exposure & contrast (along with adjustments to highlights, shadows, blacks and whites...usually try Auto first and go from there)
-Color saturation, Clarity, and Vibrance
-Save metadata file and export to JPEG

I haven't gotten in to any more advanced editing in Photoshop yet...just been doing everything in Lightroom.