ok , thats because you have a "/" at the end of the domain, so to accept that modify the Regex as per the code below;

Code:
        Dim Info() As String = System.IO.File.ReadAllLines("MyFile.txt")

        Dim Sites As New List(Of String)
        Dim Hits As New List(Of Integer)

        Dim matches As MatchCollection

        For Each s As String In Info

            Dim r As New Regex( _
            "(?<=http://www.)[A-Z0-9.-]+\.(?:[A-Z]{2}|com|org|net|gov|mil|biz|info|mobi|name|aero|jobs|museum)(?=/\s)", _
            RegexOptions.IgnoreCase Or RegexOptions.Singleline)
            matches = r.Matches(s)
            If matches.Count > 0 Then
                Dim Domain As String = matches(0).ToString
                If Not Sites.Contains(Domain) Then
                    Sites.Add(Domain)
                    Hits.Add(1)
                Else
                    Hits(Sites.IndexOf(Domain)) += 1
                End If
            Else
                'No domain was found on the line
            End If
        Next

        Dim Str As String = String.Empty
        For i As Integer = 0 To Sites.Count - 1
            Str += Sites(i) & " has " & Hits(i).ToString & " hits" & ControlChars.NewLine
        Next
        MessageBox.Show(Str)