Is OSCommerce outdated?
That depends on how you would define outdated. If you are using a v1.0, then yes. But osCommerce is still actively maintained and developed. The current development version is osCommerce 3.0 Alpha 5.
I recently started working for a web development company that uses it a lot and I noticed the code base is really messy and has a lot of older php code in there. Being used to something nice like cakePHP or drupal I wasn't too impressed with it.
I am sure you can find prettier architectures. I looked at the source code briefly and can confirm there is a number of things considered code smells nowadays, like lots of defined constants, global keywords and such. The codebase is old-fashioned compared to today's standards, but that's the way it is with long running systems that have evolved over many years. Old fashioned doesnt necessarily mean outdated though.
Is it worth using any more? Is there a decent port of OSC that is updated and easy to transfer existing stores to? bonus points if it has a plug in system that isn't a hack fest.
osCommerce is a mature product. And like said in the beginning, it is actively maintained. You shouldnt base the application's worth on the codebase alone. Wordpress would be worthless then. And CakePHP isnt exactly famous for it's codebase either. A client you will install ocCommerce for is rarely interested in the codebase, but rather in if the system can satisfy his or her requirements to a shop system.
Right now I'm looking at Zen-cart, Ubercart and Magento as alternatives. Would you recommend anything else?
There is also xtCommerce which forked from osCommerce a few years ago. This is not meant as recommendation though. I find it hard to recommend a shop system from the vast amount of systems out there without knowing any requirements.
On a sidenote: if you want to collect software metrics about osCommerce, head over to phpqatools.org and run some tools over, gather statistics and compare it to some other shop systems.