class Category(models.Model):
    ...
    category = models.CharField(max_length=70)
    
    def __unicode__(self):
        return self.category

class Project(models.Model):
    ...
    category = models.ForeignKey(Category)
    freelance_site = models.ForeignKey(FreelanceSite)
    
    def __unicode__(self):
        return self.title

class UsersCategory(models.Model):
    user = models.ForeignKey(User)
    categories = models.ManyToManyField(Category, verbose_name='Категории')
    
    def __unicode__(self):
        return self.user.username

user_category_list = UsersCategory.objects.get(user=request.user)
f_site = FreelanceSite.objects.get(id=site_id)
project_list = Project.objects.filter(freelance_site=f_site,category=user_category_list.categories).order_by("-pub_date")

ids = [cathegory.id for cathegory in user_category_list.categories] # В общем, перебираем все категории и вносим их id в список
project_list = Project.objects.filter(freelance_site=f_site,category__id__in=ids).order_by("-pub_date")