I have done a little research on WordPress plugins for eCommerce. The following two seem to be the most popular and they are both WordPress 3.0 compatible.
WP e-Commerce – A popular (947,964 downloads so far ) shopping cart option for WordPress blogs which makes it easy to sell things like ebooks, mp3s, clothing, crafts and more. The WordPress.org rating is only 3 stars based on 387 ratings.
It can be extended by premium plugins offered by GetShopped.org
eShop – Not as popular as WP e-Commerce ( only 209,393 so far ) , but is rated higher 4+ stars based on 127 reviews. Gives you the ability to add a PayPal powered store to your site. Allows one item per post or page.