I need to have 1 application per client database,suppose i had a application,i want to run it in different departments with with different DB's
but it should create a session factory at run time based on request..or some way to have more than 1 session factories...how it can be possible is any 1 having solution for this ?

cfg.xml file per client
from the code you create 2 config object as follow -
configDB1 = new Configuration ().configure("filename1.cfg.xml");
configDataBase2 = new Configuration ().configure("fileName2.cfg.xml");