Create code first, many to many, with additional fields in association table

The code provided by this answer is right, but incomplete, I've tested it. There are missing properties in "UserEmail" class:

    public UserTest UserTest { get; set; }
    public EmailTest EmailTest { get; set; }

I post the code I've tested if someone is interested. Regards

using System.Data.Entity;
using System;
using System.Collections.Generic;
using System.ComponentModel.DataAnnotations;
using System.ComponentModel.DataAnnotations.Schema;
using System.Linq;
using System.Web;

#region example2
public class UserTest
{
    public int UserTestID { get; set; }
    public string UserTestname { get; set; }
    public string Password { get; set; }

    public ICollection<UserTestEmailTest> UserTestEmailTests { get; set; }

    public static void DoSomeTest(ApplicationDbContext context)
    {

        for (int i = 0; i < 5; i++)
        {
            var user = context.UserTest.Add(new UserTest() { UserTestname = "Test" + i });
            var address = context.EmailTest.Add(new EmailTest() { Address = "address@" + i });
        }
        context.SaveChanges();

        foreach (var user in context.UserTest.Include(t => t.UserTestEmailTests))
        {
            foreach (var address in context.EmailTest)
            {
                user.UserTestEmailTests.Add(new UserTestEmailTest() { UserTest = user, EmailTest = address, n1 = user.UserTestID, n2 = address.EmailTestID });
            }
        }
        context.SaveChanges();
    }
}

public class EmailTest
{
    public int EmailTestID { get; set; }
    public string Address { get; set; }

    public ICollection<UserTestEmailTest> UserTestEmailTests { get; set; }
}

public class UserTestEmailTest
{
    public int UserTestID { get; set; }
    public UserTest UserTest { get; set; }
    public int EmailTestID { get; set; }
    public EmailTest EmailTest { get; set; }
    public int n1 { get; set; }
    public int n2 { get; set; }


    //Call this code from ApplicationDbContext.ConfigureMapping
    //and add this lines as well:
    //public System.Data.Entity.DbSet<yournamespace.UserTest> UserTest { get; set; }
    //public System.Data.Entity.DbSet<yournamespace.EmailTest> EmailTest { get; set; }
    internal static void RelateFluent(System.Data.Entity.DbModelBuilder builder)
    {
        // Primary keys
        builder.Entity<UserTest>().HasKey(q => q.UserTestID);
        builder.Entity<EmailTest>().HasKey(q => q.EmailTestID);

        builder.Entity<UserTestEmailTest>().HasKey(q =>
            new
            {
                q.UserTestID,
                q.EmailTestID
            });

        // Relationships
        builder.Entity<UserTestEmailTest>()
            .HasRequired(t => t.EmailTest)
            .WithMany(t => t.UserTestEmailTests)
            .HasForeignKey(t => t.EmailTestID);

        builder.Entity<UserTestEmailTest>()
            .HasRequired(t => t.UserTest)
            .WithMany(t => t.UserTestEmailTests)
            .HasForeignKey(t => t.UserTestID);
    }
}
#endregion

I'll just post the code to do this using the fluent API mapping.

public class User {
    public int UserID { get; set; }
    public string Username { get; set; }
    public string Password { get; set; }

    public ICollection<UserEmail> UserEmails { get; set; }
}

public class Email {
    public int EmailID { get; set; }
    public string Address { get; set; }

    public ICollection<UserEmail> UserEmails { get; set; }
}

public class UserEmail {
    public int UserID { get; set; }
    public int EmailID { get; set; }
    public bool IsPrimary { get; set; }
}

On your DbContext derived class you could do this:

public class MyContext : DbContext {
    protected override void OnModelCreating(DbModelBuilder builder) {
        // Primary keys
        builder.Entity<User>().HasKey(q => q.UserID);
        builder.Entity<Email>().HasKey(q => q.EmailID);
        builder.Entity<UserEmail>().HasKey(q => 
            new { 
                q.UserID, q.EmailID
            });

        // Relationships
        builder.Entity<UserEmail>()
            .HasRequired(t => t.Email)
            .WithMany(t => t.UserEmails)
            .HasForeignKey(t => t.EmailID)

        builder.Entity<UserEmail>()
            .HasRequired(t => t.User)
            .WithMany(t => t.UserEmails)
            .HasForeignKey(t => t.UserID)
    }
}

It has the same effect as the accepted answer, with a different approach, which is no better nor worse.

It's not possible to create a many-to-many relationship with a customized join table. In a many-to-many relationship EF manages the join table internally and hidden. It's a table without an Entity class in your model. To work with such a join table with additional properties you will have to create actually two one-to-many relationships. It could look like this:

public class Member
{
    public int MemberID { get; set; }

    public string FirstName { get; set; }
    public string LastName { get; set; }

    public virtual ICollection<MemberComment> MemberComments { get; set; }
}

public class Comment
{
    public int CommentID { get; set; }
    public string Message { get; set; }

    public virtual ICollection<MemberComment> MemberComments { get; set; }
}

public class MemberComment
{
    [Key, Column(Order = 0)]
    public int MemberID { get; set; }
    [Key, Column(Order = 1)]
    public int CommentID { get; set; }

    public virtual Member Member { get; set; }
    public virtual Comment Comment { get; set; }

    public int Something { get; set; }
    public string SomethingElse { get; set; }
}

If you now want to find all comments of members with LastName = "Smith" for example you can write a query like this:

var commentsOfMembers = context.Members
    .Where(m => m.LastName == "Smith")
    .SelectMany(m => m.MemberComments.Select(mc => mc.Comment))
    .ToList();

... or ...

var commentsOfMembers = context.MemberComments
    .Where(mc => mc.Member.LastName == "Smith")
    .Select(mc => mc.Comment)
    .ToList();

Or to create a list of members with name "Smith" (we assume there is more than one) along with their comments you can use a projection:

var membersWithComments = context.Members
    .Where(m => m.LastName == "Smith")
    .Select(m => new
    {
        Member = m,
        Comments = m.MemberComments.Select(mc => mc.Comment)
    })
    .ToList();

If you want to find all comments of a member with MemberId = 1:

var commentsOfMember = context.MemberComments
    .Where(mc => mc.MemberId == 1)
    .Select(mc => mc.Comment)
    .ToList();

Now you can also filter by the properties in your join table (which would not be possible in a many-to-many relationship), for example: Filter all comments of member 1 which have a 99 in property Something:

var filteredCommentsOfMember = context.MemberComments
    .Where(mc => mc.MemberId == 1 && mc.Something == 99)
    .Select(mc => mc.Comment)
    .ToList();

Because of lazy loading things might become easier. If you have a loaded Member you should be able to get the comments without an explicit query:

var commentsOfMember = member.MemberComments.Select(mc => mc.Comment);

I guess that lazy loading will fetch the comments automatically behind the scenes.

Edit

Just for fun a few examples more how to add entities and relationships and how to delete them in this model:

1) Create one member and two comments of this member:

var member1 = new Member { FirstName = "Pete" };
var comment1 = new Comment { Message = "Good morning!" };
var comment2 = new Comment { Message = "Good evening!" };
var memberComment1 = new MemberComment { Member = member1, Comment = comment1,
                                         Something = 101 };
var memberComment2 = new MemberComment { Member = member1, Comment = comment2,
                                         Something = 102 };

context.MemberComments.Add(memberComment1); // will also add member1 and comment1
context.MemberComments.Add(memberComment2); // will also add comment2

context.SaveChanges();

2) Add a third comment of member1:

var member1 = context.Members.Where(m => m.FirstName == "Pete")
    .SingleOrDefault();
if (member1 != null)
{
    var comment3 = new Comment { Message = "Good night!" };
    var memberComment3 = new MemberComment { Member = member1,
                                             Comment = comment3,
                                             Something = 103 };

    context.MemberComments.Add(memberComment3); // will also add comment3
    context.SaveChanges();
}

3) Create new member and relate it to the existing comment2:

var comment2 = context.Comments.Where(c => c.Message == "Good evening!")
    .SingleOrDefault();
if (comment2 != null)
{
    var member2 = new Member { FirstName = "Paul" };
    var memberComment4 = new MemberComment { Member = member2,
                                             Comment = comment2,
                                             Something = 201 };

    context.MemberComments.Add(memberComment4);
    context.SaveChanges();
}

4) Create relationship between existing member2 and comment3:

var member2 = context.Members.Where(m => m.FirstName == "Paul")
    .SingleOrDefault();
var comment3 = context.Comments.Where(c => c.Message == "Good night!")
    .SingleOrDefault();
if (member2 != null && comment3 != null)
{
    var memberComment5 = new MemberComment { Member = member2,
                                             Comment = comment3,
                                             Something = 202 };

    context.MemberComments.Add(memberComment5);
    context.SaveChanges();
}

5) Delete this relationship again:

var memberComment5 = context.MemberComments
    .Where(mc => mc.Member.FirstName == "Paul"
        && mc.Comment.Message == "Good night!")
    .SingleOrDefault();
if (memberComment5 != null)
{
    context.MemberComments.Remove(memberComment5);
    context.SaveChanges();
}

6) Delete member1 and all its relationships to the comments:

var member1 = context.Members.Where(m => m.FirstName == "Pete")
    .SingleOrDefault();
if (member1 != null)
{
    context.Members.Remove(member1);
    context.SaveChanges();
}

This deletes the relationships in MemberComments too because the one-to-many relationships between Member and MemberComments and between Comment and MemberComments are setup with cascading delete by convention. And this is the case because MemberId and CommentId in MemberComment are detected as foreign key properties for the Member and Comment navigation properties and since the FK properties are of type non-nullable int the relationship is required which finally causes the cascading-delete-setup. Makes sense in this model, I think.