I was just looking this up recently!
Massdrop were kind enough to put the full part number of the diodes they use on the
ergodox assembly page. I can guarantee that these'll work. They are diodes inc part number 1N4148W-7-F
Mouser has them for $.063 each in qty 100. Expensive!
here they are on digikey
Looking at datasheets, I found out that most, if not all standard SOD-123 diodes should fit on the pads. The diodes that massdrop have are unusually short, so you may have some clearance issues (with taller diodes, like the ones below) if you go without a case. They will fit fine inside a massdrop or similar layer case.
Based on those findings, I noticed the following
diodes on eBay $20 shipped for a thousand? I'm building a ton of keyboards? sure!
Now I don't normally trust random parts coming out of china, but these actually have a real manufacturer who has published a datasheet on them (the seller has them incorrectly listed as 1N4141WS, when in reality they are 1N4148W-T4 (by reading the picture). The T4 designation leads to the company galaxy diode, and I found a datasheet
hereEdit: ebay listing had ended: updated