The question of using a Set or a List is much more difficult I think. At least when you use hibernate as JPA implementation. If you use a List in hibernate, it automatically switch to the "Bags" paradigm, where duplicates CAN exist.
And that decision has significant influence on the queries hibernate executes. Here a little example:
There are two entities, employee and company, a typical many-to-many relation. for mapping those entities to each other, a JoinTable (lets call it "employeeCompany") exist.
You choose the datatype List on both entities (Company/Employee)
So if you now decide to remove Employee Joe from CompanyXY, hibernate executes the following queries:
delete from employeeCompany where employeeId = Joe;
insert into employeeCompany(employeeId,companyId) values (Joe,CompanyXA);
insert into employeeCompany(employeeId,companyId) values (Joe,CompanyXB);
insert into employeeCompany(employeeId,companyId) values (Joe,CompanyXC);
insert into employeeCompany(employeeId,companyId) values (Joe,CompanyXD);
insert into employeeCompany(employeeId,companyId) values (Joe,CompanyXE);
And now the question: why the hell does hibernate not only execute that query?
delete from employeeCompany where employeeId = Joe AND company = companyXY;
The answer is simple (and thx a lot to Nirav Assar for his blogpost): It can't. In a world of bags, delete all & re-insert all remaining is the only proper way! Read that for more clarification. http://assarconsulting.blogspot.fr/2009/08/why-hibernate-does-delete-all-then-re.html
Now the big conclusion:
If you choose a Set instead of a List in your Employee/Company - Entities, you don't have that Problem and only one query is executed!
And why that? Because hibernate is no longer in a world of bags (as you know, Sets allows no duplicates) and executing only one query is now possible.
So the decision between List and Sets is not that simple, at least when it comes to queries & performance!