It's been about 4 years since I've done anything with Hibernate, so I'm very rusty. I have the following schema as an example:

create table employee
(
id integer primary key auto_increment,
name varchar(64) not null,
job_title integer not null
);

create table job_title
(
id integer primary key auto_increment,
name varchar(64)
);

create table employee_job_title
(
id integer primary key auto_increment,
title_id integer not null,
employee_id integer not null
);

alter table employee_job_title add foreign key(title_id) references job_title(id);
alter table employee_job_title add foreign key(employee_id) references employee(id);

Assuming I have a class "Employee" with a method like setJobTitle(JobTitle title), how would I set up the mappings for Employee and JobTitle so that it would link them through the employee_job_title table?

You can define it using @ManyToMany
Please read the tutorial http://docs.jboss.org/hibernate/stable/annotations/reference/en/html_single/