I have implemented listeners to audit changes to tables in my application using IPreUpdateEventListener and IPreInsertEventListener and everything works except for my many-to-many relationships that don't have additional data in the joining table (i.e. I don't have a POCO for the joining table).

Each auditable object implements an IAuditable interface, so the event listener checks to see if a POCO is of type IAuditable, and if it is it records any changes to the object. Look up tables implement an IAuditableProperty inteface, so if a property of the IAuditable POCO is pointing to a lookup table, the changes are recorded in the log for the main POCO.

So, the question is, how should I determine I'm working with a many-to-many collection and record the changes in my audit table?

//first two checks for LastUpdated and LastUpdatedBy ommitted for brevity
else if (newState[i] is IAuditable)
{
    //Do nothing, these will record themselves separately
}
else if (!(newState[i] is IAuditableProperty) && (newState[i] is IList<object> || newState[i] is ISet))
{
    //Do nothing, this is a collection and individual items will update themselves if they are auditable
    //I believe this is where my many-to-many values are being lost
}
else if (!isUpdateEvent || !Equals(oldState[i], newState[i]))//Record only modified fields when updating
{
    changes.Append(preDatabaseEvent.Persister.PropertyNames[i])
        .Append(": ");
    if (newState[i] is IAuditableProperty)
    {
        //Record changes to values in lookup tables
        if (isUpdateEvent)
        {
            changes.Append(((IAuditableProperty)oldState[i]).AuditPropertyValue)
                 .Append(" => ");
        }
        changes.Append(((IAuditableProperty)newState[i]).AuditPropertyValue);
    }
    else
    {
        //Record changes for primitive values
        if(isUpdateEvent)
        {
            changes.Append(oldState[i])
                .Append(" => ");
        }
        changes.Append(newState[i]);
    }
    changes.AppendLine();
}