EF отличная ошибка (IEqualityComparer)

If you're providing your own comparisons, you'll need to execute the Distinct call in .NET code. To make sure that happens, use AsEnumerable to turn IQueryable into IEnumerable:

var result = myEntity.MyDomainEntity
        .Where(myDomainEntity => myDomainEntity.MySpecialID > default(int))
        .AsEnumerable()
        .Distinct(new FooComparer());

Of course at that point you'll be pulling more data across from the database. An alternative is to group the data instead:

var result = from entity in myEntity.MyDomainEntity
             where entity.MySpecialID > 0
             group entity by entity.MySpecialID into groups
             select groups.FirstOrDefault();

That will get you the first entity encountered with each ID (assuming my query-fu isn't failing me). That's basically what Distinct does anyway, but it's all at the database.

(Note to future readers: calling First() makes more sense than FirstOrDefault(), but apparently that doesn't work.)