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Synk
In general, I like full-blown applications more than utility wrappers. Although both are functional, the application tends to work better over time and OS changes. Wrappers need to be updated with the latest version of the underlying utility to reflect any changes made in the engine that is really doing the work. An application contains all the logic and methods that are needed to do something. It has no external dependencies (a wrapper does).
Synk is such an application. Written by Benjamin Rister, who is a graduate student at Carnegie Mellon, it is an application built from the ground floor up just to do syncing of files. It's available for a $20 single-user, non-commercial license.
Figure 2 shows the main screen setup of synchronizing a folder that lives on my main machine to a folder on my shuffle (which has the volume name of Larry Loeb). The rest of the tabs are for other program functions. The tabbed organization of the program keeps the display screens simple, without too much information showing up to confuse you during use.
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The simplicity of the UI should not blind you to the powerful features available. Although you can schedule the syncs, you can also establish rules about exactly which files are synchronized.
The rule editor allows simple creation of the rules, although earlier rules do have priority over the later ones. As you can see in Figure 3, a wide range of options to build a rule is present. The rules allow a fairly fine-grained control over what exactly gets synchronized or backed up. This is a very useful thing to have when the available space is limited, like on the shuffle.
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Synk also allows you to set the way deletions in the source folder are handled. The destination can match it or you can leave the files alone. Your choice.
In short, Synk handles most of what the average user wants to do with their files.