I use git to upload my changes to a staging website on the same server, after testing I then push it to the production website. None of the files are changed until they are all received. On the plus side, it only sends the changes compressed, so I don't even have to send an entire file.
The staging area isn't required. I work with a lot of servers and sometimes some of the specific configurations on that server (mostly just find that an extension isn't installed)/
I'm sure you can do the same with another version control system. You need to be careful though. The tutorial I linked specifically stores the git information OUTSIDE the document root. Otherwise someone can just clone all the source code for your website.
If you like SVN, the .svn being in every directory can be a little annoying. Make sure that people can't download what they shouldn't be able to.