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Microsoft offers a number of data sync options. The latest is Live Mesh [mesh.com]. This will sync data among multiple machines. You install the widget on each machine and the data syncs automatically. It rarely asks for advice about overwrites these days. In earlier versions of this beta I would get a lot of dialog boxes asking if I wanted to overwrite certain files. That doesn't happen much anymore.
An older sync tool was FolderShare [foldershare.com], but that has now become Windows Live Sync [sync.live.com]. This is confusingly similar to the Mesh product. In my experience the FolderShare product had more limitations in terms of the number of files that you could sync. However, both work reasonably well. In older versions of this software you could set it to confirm any overwrites or updates. I'm not sure about its new incarnation.
SyncToy [microsoft.com] is another MS tool that was originally developed as an unsupported PowerToy. SyncToy is becoming more automatic according to what I've read, but you can set a lot of parameters to determine what gets synced. The software also places overwritten (synced) files to the recycle bin.
These solutions might be a bit too automatic for you though. A lot of the sync software is moving in that direction. If you want real fine grained control then I usually use batch files.
I am not sure that I may (on my own) write a batch file to do the job; I kind of became DOS deficient :)
I have most of my data at my home office on the NAS. The beauty part is that it doesn't matter which machine I'm on. The data is available .
I'd even advocate running a small home server instead. I've done that myself. Take an old PC and toss in a few hard drives and then use that server as your data storage point. Microsoft makes and excellent product called Windows Home Server [microsoft.com] that will backup every machine on your network. There are also many free Linux options if you don't mind the learning curve.