GNOME 3 and Ubuntu’s soon-to-be released Unity are the first GNOME desktops designed from the start with usability principles in mind. Not that releases in the GNOME 2 series ignored usability, but in GNOME 2, usability was an addition to the desktop, comparable to adding the foundation after the house was built.
Whether you use GNOME 3 or Unity will probably depend on your distribution’s choice. But assuming you have a choice, which should you use? Suggesting an answer is hard, because in many ways the two are distinctly similar in design, with the differences largely in the details.
Which you prefer will have little to do with the applications available. Contrary to what some imagine, both are shells — different interfaces that interact with mostly the same GNOME backend and applications. A few utilities, like Unity’s Main Menu editor, are specific to the shell being used, but most of the software will be the same regardless of the interface with which you interact with it.