Annoyingly, the scanner is completely unsupported under Linux, so I'm having to do this all with Windows. After looking around at the free options for a while, I settled on using the bundled "CanoScan Toolbox" software which mostly works quite well and integrates with buttons on the scanner so I don't have to change focus on my PC to the application to tell it to scan the next page.
In the process of using it heavily, I have discovered that
- it leaks virtual memory, so you have to restart it every 100-200 pages or it hits the 2GB limit! Naturally you discover this when it has a whole lot of pages you just scanned sitting in memory which you now can't save.
- it seems to use a quadratic time algorithm for writing PDF files to disk.
So all in all it's not going too badly, as long as I only scan long things in batches of 50 pages or so and remember to restart it every so often. It's a shame that stupid things like this spoil what's generally a reasonably usable piece of software.