There are commercial programs that specialize in sync'ing folders between systems. The one I use is Synk Pro, found at www.decimus.net.
Synk Pro allows either folder sync or Master -> Slave copying, so that one folder is designated as the primary repository. Synk Pro can also remain running while the computer is on, keeping designated folders in sync.
But there potential problems synchronizing home accounts across different machines. The first one that comes to mind is ~/Library/Preferences, which stores the default setup information for your system: some of the settings may not work properly on different machines. The Mail folders in ~/Library could easily lead to data loss: if you update Mail on both systems inadvertently, then synchronizing the folders could result in overwriting messages in one folder with different contents. This can be avoided if you only retrieve mail on one system, and copy that Mail setup to the other machine. If you only synchronize user folders, like Documents and Downloads, most of such pitfalls are avoided.
There are also companies that provide data file sync through the internet, by copying your files to their servers, and then copying from their servers to the other systems you select, and authorize by password. Two examples of these are Dropbox and www.sugarsync.com.
These services cannot guarantee synchronization if you have the same file open on two machines, however. There are some programs designed to work with Dropbox, that allow changes made on one computer to automatically show up on another machine; for example, 1password or TextExpander. But many programs are not so designed: Apple programs like Pages and Numbers will not work this way. You must close the file on all machines before the file can be sync'ed. And it should have been opened on only one machine at a time. And these services require $$ per year for large amounts of content. Dropbox provides free accounts for up to 2 GB of data, so you could try their service for free to see if it meets your needs. It has been very reliable for me.
SugarSync is designed to sync files through the internet and provide offline backup. It has been working well after some initial problems, when their Mac program was still in beta. Both these services allow you to sync files to Windows based machines also. And both allow retrieving previous file versions from their servers.
Note that if a machine has been shutdown, it may take a long time to complete the updates over your internet connection. My desktop remains running even if I am away from my desk.
