My first real job working with PHP, MySQL, and an actual server backend was with an ecommerce integration company Kosmos Central, who created an API that hooks point of sale systems and inventories with an online salefront. The default integration was with the open-source ecommerce package X-Cart, and it was there that I cut my teeth on databasing, user stories, debugging, and template systems (via Smarty).
I worked with an in-house designer for most of our clients, and this is where I found my love of design implementation, going through continual feedback and iterative designs while satisfying client demands. Although Kosmos did not use any actual version control, this is also where I learned SVN and Git and made my choice as to which I preferred to work with. Ecommerce itself is also a complicated beast, in my opinion, featuring a system that has to make calls "outside of the house" in order to process payments or utilize single sign on services, which opposes most of the CMS work that I've done since then.
I don't believe any of these sites have survived through the years since I've worked on them, but I still hold on to a number of screenshots and quite a good bit of documentation.