Ah, you went ahead and created the topic. Good. I was intending to do it, but after mulling some things over… 
@Lee_Travis, my apologies for hijacking the other thread.
Last night I spent coding up some high level suggestion for a smart contract decentralized exchange, based partly on ideas I had a couple of months ago - very similar in the gist to this description by @intrz.
It’s high level in the way that it leaves out the details about the underlying storage/framework (SAFENetwork in this case). Furthermore it simulates agents running the code on separate machines, as actors in the same process. So a lot of simplification. A lot.
The need for atomicity in the transfer step is removed by letting the contracts take ownership of the tokens put up for trade.
I would really like to share the code as to continue refine the idea by reasoning about the code.
I find that I kind of think and communicate more fluently in code… 
But I want to tie up the loose ends and run simulations on it before I put it up!
Continuing on the subject from that topic:
I’m not convinced by the response from Bancor ppl to the criticism by prof. E. Gün Sirer.
It’s worth trying to use it somehow anyway.
One thing that is not mentioned at all, is that the necessary arbitrageurs will have little effect if there is no other place to exchange the token. So the long tail that would be helped is still needing to be served in some sort of exchange, which they are not, and this is the problem Bancor was supposed to solve.
I think a Bancor-like network absolutely has to be combined with a(t least one) decentralized exchange. NB that there is still no guarantee that the arbitrageurs can do their supposed work, as they still need liquidity elsewhere for this. But the possibility to remove the listing threshold (token volume so low that the fees from it would not compensate the listing overhead) is there when we go decentralized. At least that’s my initial view.
I discern three different subjects here, where the last one, as I see it, is that of the OP Title.
- SmartTokens
- Decentralized exchanges
- In app token agnosticism
The combination of 1. and 2. is what will enable 3. IMO, with some nifty coding.