I have used two approaches
1) Write a perl script to rename, use Picasa to organise.
2) Stop worrying about filenames, use Picasa to organise into folders named by date
See also https://superuser.com/questions/28646/how-do-you-manage-your-personal-photos-in-windows
EDIT
Here's why I thought Picasa might be useful.
Rename (documents scanned as) JPEG images : in Picasa, select a group of images and choose "Rename" from the "File menu". I havent used this, so I imagine it is less flexible than some other renaming tools.
Organise (documents scanned as) JPEG images : Picasa lets you attach tags to images, you can later select photos using these tags. The tag data is stored in the EXIF (I think) data in the JPEG file. You can also place images or groups of images into arbitrary folders. You can also create virtual folders (Picasa calls them albums) so that an image might appear in a "contracts" folder as well as a "Acme Inc" folder and a "Trunnion" folder.
View and Browse batches of images : If batches are placed in (say) a "recently scanned" folder, Picasa allows you to view and browse those images prior to reorganising them into other folders.
Batch rename : In Picasa select a group of images and press F2 (untried).
Index images : see tags above
Organise into folders : see above
Collate, Organise, Curate the results: see above for collating and organising. I am ignorant about curating - perhaps specialist software is needed.
Archival : you can export groups of images. I believe it can create CDs or DVDs optionally including viewer software (which doesn't stop you viewing folders of JPEGs using any other tool). Picasa does store some metatdata in picasa.ini files - but I think this is limited to image modifications (the original files is normally left unchanged). I believe the tag and some other metadata is stored in standard parts of the EXIF section in the JPEG image itself - so other applications can in principle retrieve it.
However I accept that Rob has more specialised needs.
Didn't think of IrfanView, well it's a thought now! Thanks for the additional option, I will look further into it later with more time. Didn't know about this tagging feature in the EXIF, though my main need is for the file itself to have a meaningful name, e.g. Project - page 1 of 4.jpg, Project - page 2 of 4.jpg ... – therobyouknow – 2010-11-05T13:30:05.047