I have a custom content type with some custom site columns. I can't find anywhere to reorder the columns for the content type. How can this be done in Sharepoint Designer 2010? Thanks.
you cannot do it from SharePoint Designer. You have to do it from browser interface. From Site Settings --> Content Types Page.
Keep in mind that you may not be able to do everything from SPD that you can do from browser interface and vice versa.
you can use "Column Order" link under "Columns" section in Manage Content Type page (_layouts/ManageContentType.aspx?ctype=0x0100EDB28B537320E749881D67FD6A9AD47C). You can also came there directly by the following URL: _layouts/ChangeFieldOrder.aspx?ctype=0x0100EDB28B537320E749881D67FD6A9AD47C (please insert ID of your content type there)