There are several ways to remedy this, one of them is by using attribute editor (there's a small comment box in the bottom)

I recently found a free software called FileHamster. What it does is basically save the backup of your current scene, and allow you to give comments, or notes, and also lock the file, so that it's not easily edited.

What you see here, is that I ask FileHamster(FH) to watch a folder called c:\Documents...\scenes, and in that folder I have only 1 file, which is test_V01.mb
test_V01.mb only have a sphere in a scene. I save the file.
The popup will appear, asking what comment you wanna write, so I write "a scene..."
Next, I add a cube to the scene, and save again. This time I still save the scene as test_V01.mb, instead of test_V02.mb, which was my typical workflow. The popup appear again, asking for comment, so I add "tambah cube".
I did the same thing again by adding cone.. and the process goes on.
The benefit here is that I only have a file on my working directory, instead of several versions, which is of course, neato!
There is a good example on using FH with Photoshop in their website, I suggest.. give it a try :)