Hi Tom
It took a while but I got there in the end. I was using joomla 1.5 and I downloaded a component called "tag meta" which allows you to insert tags including the canonical tag on specific urls or more importantly urls which begin in a certain way. Now how you use it depends on how your sef urls are set up or what sef component you are using but you can put a canonical tag on every url in a section that has view-all-products in it.
So in one of my examples I put a canonical tag pointing to /maternity-tops.html (my main category page for that section) on every url that began with /maternity-tops/view-all-products
I hope this if of help to you. It takes a bit of playing around with but it worked for me. The component also has fairly good documentation.
Regards
Damien