It depends, if it's a small scale site for a couple of apps or something, WordPress is the way to go. However, mainly for security purposes, if it's larger I would say Joomla.
Joomla has been around forever and it's far more developed as far as a true CMS goes. WordPress is getting there and will be there one day, but for now it's still a blog that's able to do some cool stuff.
The thing is with Joomla, right now I'd say it's at a crossroads. There's a lot of extensions for it, but when it comes to ecommerce I'd suggest checking out Ecwid. IF, you're planning on this site for the long haul that is.
Because Ecwid offers some very cool features and capabilities (and is also compatible with any CMS, btw, and free as well) however it's ajax powered. Which means Google JUST became able to potentially index its content. Ecwid has a built in catalog that Google will index, but this catalog fucks up your URL structure. (If that doesn't bother you, disregard all the negative things I have to say about Ecwid).
With Joomla, it's best to have the menu power everything and if you know what you're doing, you can have multiple menus on the front end all called from a single menu using levels. You can't do this with Ecwid's SEO catalog, which means you cannot control key things like... Page title, meta tags, URL, etc.
So it's really which way you want to go and wait.. I decided to go with the menu structure controlling my site. So I won't have to do it later, it's much better for SEO. However Google can't see my category/product content yet and I'm stuck there until I can either workaround it or those Russians get sick of hearing me bitch about their shitty SEO out of the box and do whatever it is so that Google can index their ajax content.
Basically, if you go with Joomla, just be prepared to do a lot of work and have at least an intermediate understanding of CMS and PHP code. You can go with different ecommerce platforms to, but no matter what you go with it's going to be a lot of customization. However, you're site will be much more flexible, secure and stable. Plus it's a lot easier than Magento.
