I have all my tables with primary keys of type INT8 in a Postgres database.
When I use Middlegen-Hibernate-r2 to create my mapping files, I get some id's mapped with type="long" (which is correct) and other id's with type="int". Is this solved in the near release of r3?

R3 has been released. Middlegen chooses the defaults and you have the option to change it using the GUI. I suggest you launch it in GUI mode and change what is not appropriate. I may in the future include a default list for various dialects but this is not going to nesessarily satisfy all users.

Ok. But I'm dealing with 110 tables and the GUI gets a bit cluttered. My question is how does Middlegen chooses it's defaults? Because if it does, then the mapping files would have type="int" or type="long" in all of them.

The defaults are chosen only if the table has not been found before and it selects from a list of possible types including conversion types. It then uses the property preferences file to get the values. I would suggest you edit the property preferences file to set the values that you want. A sed script or other equivalent will do the job.