WooCommerce is the market leading WordPress e-Commerce plugin. It is very actively developed and supported, has tens of extensions / themes and finds widespread support from WordPress community.
Jigoshop could very well be the plugin that started the new wave of eCommerce boom based on WordPress. After all, WooCommerce was forked from it!
Cart66 was widely endorsed before Woo and Jigo arrived. If you are looking for other options, then this should be a good plugin to check.
Digital downloads and membership sites
Easy Digital Downloads seems to be the emerging favorite among WordPress geeks to sell digital goods. People like Yoast, Organic Themes use it for selling their plugins and themes.
Premise is a membership and landing page plugin from the makers of StudioPress. It comes with unique tutorials from Industry leaders on how to improve your membership based businesses.