I've been working on a project for the last few months to support wireless upload of sketches. I started this project because I had several projects that were in difficult to reach areas and I got tired of dealing with the hassle to plug in a FTDI every time I wanted to tweak the firmware. Currently it supports XBee, Wifi (ESP8266) and Nordic but other wireless or even wired (ethernet) could be supported. In a nutshell this is a two chip solution, that relies on a EEPROM to buffer the firmware prior to flashing. It uses the the Optiboot bootloader (standard on the UNO) and works with any Atmega 328/168 chip. I've provided a Java client (cross-platform) for uploading to the remote Arduino. I would say it's appropriate for more advanced users at this point, although I have made an attempt to provide the documentation to get you up and running. The project is on github
EEPROM? Sounds nifty for the Zero but I would personally look into adding support for SD.