chkApplications.SelectedValue = 2;
chkApplications.SelectedValue = 6;

chkApplications.Items.FindByValue("2").Selected = true;
chkApplications.Items.FindByValue("6").Selected = true;

foreach (ListItem item in chkApplications.Items)
    {
        if (item.Value == "2" || item.Value == "6")
        {
            item.Selected = true;
        }
    }

foreach (var item in cb.Items.Cast<ListItem>()
        .Where (li => li.Value == "2" || li.Value == "6"))
   item.Selected = true;

foreach (var item in MyList)
{
    checkBoxList.Items.FindByValue(item.id).Selected = true;
}