Well I may have to join you in that effort; I need to do the same thing as my project goes beyond the lovingly-hand-deployed-by-the-author pilot phase.
I did a little work on an STDFU-based deployment, this work was really for flashing the netduino firmware, but as I mentioned that approach can also deploy the app. Details here, as well as functioning source:
http://forums.netdui...ributors/page-3
this is an incomplete project from UI and usability, but the important bits of flashing firmware work correctly.
I also did a mostly unrelated thing -- it had to do with assigning the MAC address to a board as a manufacturing step -- but I mention it because it is a desktop app that uses the same assemblies the MFDeploy does. It might give you some ideas on the firmware deployment. Then again, quite possibly not, but you can decide if its of any use:
http://forums.netdui...el-and-barcode/
Personally, as I mentioned, I find it handy to deploy both the (netduino) firmware version with which QA tested my application, along with my applicationitself, but I can appreciate the MFDeploy approach. Plus, there's always the network settings which are easier to do via MFDeploy. Oh, and plus you don't have to hold down the button. Which may not be so accessible when its in a box.
Lastly, another of my long pending mini-projects is to replace tiny booter with a mechanism to permit over-the-air updates. I did a little work testing dynamically loading netmf assemblies. The technique works, but it is a bust for me as a methodology because all the code is then in RAM. If curious, it's described here:
http://forums.netdui...pdate-possible/
However, I am pretty sure I can make a tinybooter replacement to do it. Tinybooter is meaningful on other netmf things, but it doesn't do much on netduino. I built a firmware image with no tinybooter and it ran just fine. The only thing I know of that the tinyclr does do is allow setting of stuff in the config sector. And it can, it just doesn't. So there's 48k of code space available for something fun, like checking SD for an update image, flashing it, and rebooting.
Anyway, this is one of my ponderously long posts, and I apologize for that, but as Blaise Pascal once wrote 'I apologize that this is long, but I lacked the time to make it short'. Ha!
