To really be clear on the difference, single "full" WordPress installations allow the user/owner to control everything the visitor sees, including the look, effects, use of plugins, everything down to the finest detail.
WordPressMU is controlled by the host, not the user. You can certainly set up WordPressMU as a multiblog, but there are plugins and other tools that will allow you to do that with much more control with WordPress.
In WordPressMU, the host or administrator controls everything, what Themes can be chosen, if plugins are available or not, and all server-associated adminisration controls. The user can only choose the Look from a list, with no customization, and then only control what they post, their content. They can name their site, create link lists, categories, Pages, but they have no control over any of the details.
If you want to run several blogs on your own, then choosing the full WordPress with multiple blog add-ons will get your further than WordPressMU, I believe. If you want to host a lot of users with their own "sites", and build a community, then WordPressMU is perfect.
Does that help clear things up?