Hi! I think the right way is colored coins.
I myself studied master coin and colored coin, and I found colored coin the most solid and transparent way to go for stock market. I found that master coin is the best to demonstrate property of physical goods, but not for things that have so many elements, like shares.
For example, with master coins you can demonstrate the property of your cell phone, because you can have 1, maybe 2 or 3. But for stocks you want to demonstrate property of maybe 2000 or more shares, and there master coin fails.
On the other side, colored coins is very good to demonstrate property of big number of equal items, just like shares. And also gives some interesting possibilities, like an easy way to identify your investors and pay dividends without asking their addresses.
I'm developing an stock exchange called coinmarket.pw (also coinmarket.mx and coinmarket.bit)
There I'm using colored coins, joining with bitmessage for p2p order book and trade contact and namecoin for colored coin's metadata definition.
If you want to follow the development or buy shares of my exchange, you can contact me here, and follow this link
https://forum.litecoin.net/index.php/topic,6324.new.html#new.