If you want to wade through it, the US Census put out a comprehensive report on their view of the "Electronic Economy" earlier this year.
But without exact numbers, I can tell you there's hundreds of thousands worldwide. And that means two things for you:
My point overall is this: The number of e-commerce sites out there is not relevant to your market analysis at this stage of the game. Whether there's 100,000 or 1,000,000 of them doesn't matter.
There's enough, and you need to focus on evaluating whether you can actually make money from the ones that are out there.
I agree with Gabriel Hurley regarding the insignificance of how many there are.
You need to work on improving your target market, so, if you are looking for e-commerce sites that have revenue above or below a certain amount, then you will need to look at what you offer that they need.
I will guess you are looking for e-commerce sites that need some help to grow, then you will run into the fact that they are having problems in part due to lack of resources, and the fact that the field is so crowded that they will have a hard time standing out.
Once you have pared down your target market, then you can start to get a better idea as to how many companies might be out there for you, but remember, a company may have several e-commerce sites, so the number of sites are actually useless, the number of companies that have e-commerce sites would be more useful.
I too am trying to find information about the number of e-commerce businesses out there. I am looking for specific e-commerce retailers by product type/category. I'm pretty sure the information is not readily available.
In response to the other question, IBIS World has a report on e-commerce, and the free preview has a total number of businesses: http://www.ibisworld.com/industry/default.aspx?indid=1930 I completely understand the distinction between top down and bottom up approaches. I agree that bottom-up makes more sense, however the top down approach can help to provide a framework to structure one's thinking about an opportunity and potential business models.