When you develop solutions for SharePoint using Visual Studio, there is nothing special if you focus on SharePoint. All source files are processed as usual when you use the version control system. I used CVS, SourceGear and VSS without any problems.
But since you are asking, I wonder if you really mean the changes that you use with SharePoint Designer? Well, firstly, really think about switching to developing your customization using features and solutions in Visual Studio. You have much better control over what you changed, and I don't believe that SharePoint Designer supports version control.