Where should I put the SQL files in my Java project?

In a Java/Maven setting we use as project hierarchy:

project/src/main/java/Package/Class.java
project/src/test/java/Package/ClassTest.java
project/src/main/resources/Package/resource.properties
project/src/test/resources/Package/test_resource.properties

And in order to answer your question: I would put the SQL-files along with the resources under src/main/resources.

You may want to have a look at this thread.

I'd be tempted to put the SQL queries in a dedicated SQL folder under src. This separates the Java code from the SQL:

+ src
  + java 
  + sql
     - Package/Class.sql
+ test

Alternatively you could put them into simple properties files using the above structure:

getUserByName = select * from users where name=?

getUserByEmail = select * from users where email=?

getUserByLongQuery = select * from users where email=? \
   and something = ? \
   where something_else = ?

Also, I think it's worth mentioning that you can put multi-line strings into a Java class if you prefer to take that route:

class MyClass {
    MY_QUERY = "select * from users where email = ? " + 
               "and something_else = ?";
}