Copy listitems from one custom list to another, then move them into subfolders.

SPListItem listItem = web.GetListItem(listItemUrl);
listItem.CopyTo(destinationUrl); // Copies the item to the specified destinations

or

listItem.CopyFrom(sourceUrl); // Overwrites the current item with the specified version of the item.

SPListItem item = Web.Lists["Announcement"].GetItemById(5);
SPFile file = Web.GetFile(item.Url);
file.MoveTo("New location...with the ID_.000");