I found that the part numbers for headers in many capes and in the beagle bone BOM is hard to find with google. After a couple of days I found them.
For example BeagleBone BOM, has the header listed under MLE (which turns out to be major league electronics) and part number SSHS-123-D-02-GT-LF. I was unable to google either of thoses so I wanted to share the link. I was mostly looking for pass through sockets for a cape I am working on. MLE sells them too.
Major league electronics sells mostly in bulk so there isn’t a link on their site to order online. But after emailing them I found that they put up a store just for the beagle bone. You can find it through google if you know where to look (ie google Major League Electronics Beagle bone store). But the link is here:
For a cape header I think this is the right one: http://www.retrodesignlab.com/beaglebone/store-2/#!/~/product/category=5050080&id=21110483 (SSHQ-123-D-10-GT-LF)
I was unable to find anything on mouser or digikey. Jameco has something close but with only 40 pins (not 46). Adafruit does sell something that looks like it is equivalent here: http://www.adafruit.com/products/706 for about the same price.
Anyway just thought I would share.