Copying this from what I wrote in the user comments on EZShop at photo.net:
I purchased this scanner after returning a Minolta Dimage Scan Dual II. I like the FS4000 a lot for its image quality, but the driver's lack of scan-to-file is a pain. I have about 200 wedding photos to scan, and this makes it a severely hard task.
I've looked into VueScan, and like the program a lot, but think the scanner gets better results with regards to dust removal with the Canon driver, particularly when coupled with the use of the color profile linked from normankoren.com.
To solve the batching problem, I'm building (in final testing right now) a small MFC Windows dialog app that allows specification of an output directory, a printf formatting string for filenames, and a beginning index number. The app will increment the index each time it builds a filename, saving off as either a 24 bpp or 48 bpp tiff file each image the twain driver returns. This keeps the memory usage down to that of a single image, rather than 6x that to load all the images into an editor that acquires via twain but doesn't save them off as they arrive from the twain driver.
If there's any interest in this, I'll post the software at http://www.goof.com/~mmead/ when it's finished. I expect to have it done in the next few days - I need to get started on these scans!
If there's interest in support for more than just 24 bit or 48 bit images, I can probably add the other types that the Canon twain driver will return, but these are what I need for the moment.