Well, I can say how I've been doing it with "Dave's Quest".
The initial version of the complete game I release I will call version 1.0. Any time I make a change after that, I would increase it by .01 so an updated version would be 1.01 I wouldn't jump it up to version 2.0 unless I basically remade the game, like in SCI for example, or if I added mouse compatiblity (I'd probably never do that. Save it for SCI games).
The game before it is completed started out with version 0.0. Each time I backed it up and added it to a zip file, I increased it by .01. Just to let you know, the first work in progress I released to the public was version 0.07 The second was 0.17 So, I did 17 zipped file back-ups to that point. Regardless of that number, however, like I said, when the game is complete, I will automatically elevate it to version 1.00 So, how do I decide when to do a new zip file back up? Well, it depends. It usually has to do with how much work I've done on it. Like, have I crossed the point that if I lose my files and have to go to a back-up have I lost so much that I'll be disgruntled if I have to start again? This point usually comes when I've added about five scenes. Or, if I've worked on it two weeks straight.
I hope that this answers you're questions about version number. It's just my system.