1) Is it sufficient to use Flex Builder without Flex Data Services for
web applications like E-commerce? Will there be a low cost version of
FDS ?(If yes,is JMS possible with Flex builder.)


yes, FDS is just one of the means that you can use to communicate with the server, others include http service, remote object or simply using NetConnection and AMF.

2) Which database would you recommend for this Flex development
environment?


this doesn't really matters, our team use php/java and mysql all the time.

3) Which technology is suitable for business layer(Java or .NET )

I don't really think there's certain technology *more* suitable for Flex, because it works with every technology as the backend.

choosing a right communication strategy might be more important.
 
http service, remote object (aka flash remoting) and web service are the most popular ways to communicate with app server, and they work with virtually every major server-side technology, so you don't really have to use JSP.


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