What is the best way of implementing a web application that uses JSP, servlet and EJB technologies all together following a Model View Controller (MVC) architecture?
Hmm, 'Best Way' is a bit rough - there are several 'good' ways, and the usual set of trade-offs between them. (I'm a consultant - I have to start any answer with "It depends...", otherwise they revoke my whiteboard privileges)
The main thing you need to keep in mind as you design this sort of a system is that you want the interface into the EJB's to be rather narrow: in any flow, the ideal is to call one EJB method (hopefully on a stateless session bean), and let it make calls to entities on your behalf, then hand back the data you need to display.
Essentially, I'm saying that Entity beans are your model, your controller is Session beans (maybe with a bit of help from servlets or beans), and your JSPs, beans and servlets are your View.
One thing to note here: this discussion strongly implies that your EJBs are capable of externalizing their state as some number of very simple 'value objects' (not EJBs themselves, just something we can pass back and forth). These value objects are probably tuned tightly to a workflow, and will be produced by that session bean. This way the traffic between the EJB (server) and the JSP/Servlet (client) is tuned to what the client needs, while the transaction load on the server is minimized.