My own workflow is to copy the entire folder of images from my A100 to a drive, and rename that directory to something descriptive, usually the place or event I was shooting. I don't rename the files, as the A100 gives each one a unique name. As they are date-stamped at the moment of creation on the camera, I do not organise them by date. This entire file structure can be accessed and viewed easily using Picassa - useful for uploading to online print services. I'm a desperate hoarder, so tend not to delete files unless they are completely rubbish, and I have usually done this already in-camera, but my regular file browser (I use Nautilus on OpenSuse 11) allows me to open and delete duff shots.
I run RawTherapee 2.4m1 and browse to the new directory, and make edits on the RAW files as appropriate. This creates a .pp2 file of the same name in the same directory; this is simply a text file describing all the edits made - at present, this file doesn't distinguish RAW and JPEG files of the same name, so be wary when shooting RAW+JPEG!
At present, RT does not have batch capabilities. It does have IPTC capabilities, so extensive time and date details, credits, captions and notes can be added here. These can be copied and pasted manually to other .pp2 files. It's a good idea to put your basic details into the default postprocessing profiles, to save you doing it for each image.
Depending on the output method desired, I apply sharpening (I'm starting to use the RL convolution method in RT), output size, cropping and the appropriate colourspace, and hit save - this will by default go to a 'converted' subfolder, but can be edited to a relative or absolute file location. The final TIFF or JPEG can then be additionally edited in Photoshop or GIMP if it really needs it, and printed, uploaded, emailed or saved to external media.
For speed, I'll simply edit the camera's JPEGs in GIMP directly - this is usually for web use, where the image will be dramatically reduced in size anyway.