...or

Sub SKIP_ifcell_empty()

    Dim i As Integer

    For i = 2 To 1000
        If Cells(i, 3) <> Empty And Cells(i, 2).Value > Cells(i, 3).Value Then
            Cells(i, 2).Interior.Color = 3000
        End If
    Next i

End Sub

which avoids the need for any GoTo and the creation of 'spaghetti' code.