First of all, my gratitude for providing your patch to AsideShop which made it work on WordPress 2.8 and 2.9. You will certainly be credited for your work.
I looked through your version and I found an amazing the_post hook which actually made me headaches before. WP_Query_Asideshop was a workaround just because the_post hook was not available.
I tested your version of the plugin and I got double posts in category and tag pages because
asideshop_the_post was missing a validation by
asideshop_is_displayable (which tells whether show asides on category and tags pages).
Now, I've played a little around and implemented your solution with some backwards compatibility which will please everybody who use WordPress starting from 2.2. I will remove this compatibility soon as code becomes just too bloated with version checking, and nobody is using WP 2.5 anymore, right?
Chris, I'm not sure whether you live on the edge, but may I ask you to check out a trunk version of AsideShop and give it a try. I myself tested it in WP 2.7, 2.8 and 2.9 and all aside formatting works fine. I just need confirmation it works in the wild. If it does, AsideShop 1.1 will be released immediately.
You can check latest trunk here: http://plugins.svn.wordpress.org/asideshop/trunk/ or download it as a zip file here: http://wordpress.org/extend/plugins/asideshop/download/ (Development Version)
Cheers, let me know how it works for you.