If you wish to use the Hibernate 3.6 libraries, what you could do is download Hibernate 3.6 JARs and create a User library containing these JARs. Then, for the project which contains the Hibernate 3.1 libraries, on the Java > Build Path properties page, remove the 3.1 containers and replace them with the User Libraries you created. Of course, you could just add the JARs to the build path directly, without creating an intermediate user library. I assume you are doing something like this already, is there any specific 3.6 support that you are looking for?
I realize this is not the best solution, but given that we are behind our Hibernate releases, we are contemplating adding support for the most recent version of Hibernate, Hibernate 4.1 in the next version of MyEclipse and skipping missed versions like 3.5 and 3.6 in order to keep our build size down.